Immunogenic polypeptide isolated from mycobacterium avium subspecies paratuberculosis and uses therof

ABSTRACT

The present invention relates to an immunogenic polypeptide isolated from Mycobacterium avium subspecies  paratuberculosis  and variants of the polypeptide. The polypeptide and variants may be used in vaccines against Johne&#39;s disease and in methods for detection of the disease. Antibodies against the polypeptide or variants may be used in diagnostic tests for Johne&#39;s disease. Also included are polynucleotides encoding the polypeptide and variants, and methods for preparing these.

This invention relates to a protein and compositions which contain it.More particularly, it relates to an exported protein identified inculture filtrate from Mycobacterium avium subspecies paratuberculosis.

BACKGROUND

Johne's disease (paratuberculosis) is a chronic wasting disease ofruminant animals caused by the bacterium Mycobacterium avium subspeciesparatuberculosis (M ptb).

The disease spreads insidiously, with animals becoming infected early inlife following ingestion of contaminated milk, collostrum, or pasture.In many countries, including New Zealand and the USA, herds are notroutinely tested for M. ptb infection. The number of herds officiallyknown to have infection is therefore thought to be a gross underestimateof the actual level of infection. Estimates suggest that approximately60% of dairy herds in New Zealand are infected with M. ptb. In sheep,prevalence of M. ptb infection may be as high as 70%.

Infected animals are less productive, which results in significanteconomic losses for farmers. The cost to New Zealand farmers isestimated to be in excess of $30 million per annum. The economic impactin the USA was estimated to be as much as US$1.7 billion per annum(Chiodini et al., 1984a).

Good management practices, herd testing, and culling of infected animalsare important tools for controlling paratuberculosis. However, thisstrategy alone is Iunlikely to completely control the problem becausecurrent diagnostic tests frequently fail to identify infected animals inthe early, preclinical stages of disease. The early stages of diseaseare asymptomatic and shedding of the organism in the faeces isundetectable or intermittent. Only animals which progress to theterminal stage generally show clinical disease, and that only after twoto five years (Stuart, 1965; Lepper et al., 1989). For this reason, itis suggested that for every clinical case on a farm, there areapproximately 20 additional infected animals.

Detection of infection in the host is influenced by the stage of disease(Ridge et al., 1991; Sweeney et al., 1995). In the lengthy preclinicalstage, the bacterium produces little or no detectable immune responseand the number of organisms is typically low, making direct detection ofthe bacterium difficult. In cattle, culture of M. ptb from faeces ortissue is currently the most accurate means of detecting infection. Thesuccess of culture is linked to the presence of sufficient numbers of M.ptb being shed from the intestine. Hence, animals in the early stages ofdisease, which do not shed the bacterium, or shed intermittently, aredifficult to detect by this method. A further disadvantage of culture isthe long incubation time required for the appearance of colonies.

Serological testing is also available, however, this performs best inanimals with clinical disease (80% detection) and poorly withpreclinically infected animals (as low as 15% detection),(Billman-Jacobe et al., 1992; Sweeney et al., 1995).

Alternatively, M. ptb can be confirmed through PCR to identify thepresence of the species-specific DNA fragments. To date, only threesubspecies-specific DNA fragments have been identified in the M a ptbgenome.

Of these, the most widely used is the IS900 element. IS900 detection byPCR is available as a commercial kit (Idexx, USA). This test is reportedto have a sensitivity of approximately 60% in infected cattle, based oncattle diagnosed by faecal culture (Whipple et al., 1992). A report offinding organisms that give positive results with IS900 PCR but are notM ptb has placed some doubt on the routine use of this test as theultimate confirmation of M. ptb (Cousins et al., 1999).

Eradication of Johne's disease is difficult due to the inability ofcurrent diagnostic tests to detect all infected animals. As aconsequence, more animals are put at risk of infection becausepreclinically infected animals intermittently shed the bacterium,thereby spreading the organism. Therefore, improvements in thesensitivity of diagnostic testing and/or increased immunity ofuninfected animals would be beneficial.

Commercially available vaccines for the control of Johne's diseasecontain whole organisms, either attenuated strains of M. ptb (eg.Neoparasec—Merial, France), or heat-killed preparations (eg. Gudair—CZVeterinaria, Porrino, Spain), which are mixed with an oily adjuvant andinjected subcutaneously. Vaccination does not prevent or eliminateinfection, but reduces the number of animals that progress to clinicaldisease and the excretion of organisms in the faeces.

Unfortunately, these whole cell vaccines come with a number ofdrawbacks. Firstly, the immunogenic load presented by the whole cell inconjunction with the adjuvant induces a severe hypersensitivity reactionat the injection site, which can cause the formation of a persistentnodule (granuloma). Occasional rupture of the nodule causes suffering tothe animal and potential downgrading of the carcass at slaughter, withconcomitant diminished returns for the farmer. Histological examinationof nodules or regional lymph nodes can reveal the presence of acid-fastorganisms that can be confused with the tuberculosis organism.Additionally, while Johne's disease is distinct from tuberculosis, andcaused by a distinct organism, the current Johne's vaccines can generatecross-reactive responses to M bovis skin test antigens which caninterfere with tuberculosis control programmes.

Accordingly, there is a need for alternative methods for detectingJohne's disease in animals, and proteins and/or markers and/or vaccinesuseful in such methods.

The applicants have identified and characterized a novel protein, fromM. ptb, which exhibits strong potential as a diagnostic marker and asubunit vaccine. A raw nucleotide sequence similar to that encoding theprotein of the invention was located in the TIGR Mycobacterium aviumsubspecies avium database. This nucleotide database was unannotated, thesequence had not been identified as an open reading fame, nor as a gene,and no protein-encoding utility had been ascribed to the raw nucleotidesequence. Accordingly, the applicants are the first to teach theidentification of this nucleotide sequence as a protein-encoding gene.The protein can be readily obtained from a culture filtrate of M. ptb,or expressed in a heterologous host, as the gene encoding this proteinhas also been identified and characterized by the applicants. It istowards this protein that the present invention is broadly directed.

SUMMARY OF THE INVENTION

Accordingly, in a first aspect the present invention provides arecombinant, purified, or isolated polypeptide which has a) the aminoacid sequence set forth in FIG. 1 (SEQ ID NO:1), or b) a functionallyequivalent variant which has greater than 77% amino acid sequenceidentity with said polypeptide, or c) a functionally equivalent fragmentof a polypeptide defined in a) or b).

Accordingly, in another aspect the present invention provides arecombinant, purified, or isolated polypeptide has a) the amino acidsequence of amino acids 20 to 235 as set forth in FIG. 1 (SEQ ID NO:1),or b) a functionally equivalent variant which has greater than 77% aminoacid sequence identity with said polypeptide, or c) a functionallyequivalent fragment of a polypeptide defined in a) or b).

Accordingly, in another aspect the present invention provides apolypeptide or functionally equivalent valiant, or functionallyequivalent fragment as defined above which is obtainable from abacterium.

Accordingly, in another aspect the present invention provides apolypeptide or functionally equivalent variant, or functionallyequivalent fragment as defined above which is obtainable fromMycobacterium avium subspecies paratuberculosis.

Accordingly, in another aspect the present invention provides apolypeptide or functionally equivalent variant, or functionallyequivalent fragment as defined above which is obtainable fromMycobacterium avium subspecies paratuberculosis ATCC 53950.

Accordingly, in another aspect the present invention provides apolypeptide as defined above which is obtainable from a heterologoushost transformed with a polynucleotide which encodes said protein orfunctionally equivalent variant or fragment thereof wherein said host iscapable of expressing said polypeptide. Preferably, the host is E. coli.

Accordingly, in another aspect the present invention provides arecombinant, purified, or isolated polynucleotide comprising thesequence set forth in FIG. 2 (SEQ ID NO:2) or a fragment or variantthereof capable of encoding a polypeptide which has a) the amino acidsequence set forth in FIG. 1 (SEQ ID NO: 1), or b) a functionallyequivalent variant which has greater than 77% amino acid sequenceidentity with said polypeptide, or c) a functionally equivalent fragmentof a polypeptide defined in a) or b).

Accordingly, in another aspect the present invention provides a geneticconstruct comprising (a) a promoter sequence; (b) an open reading framepolynucleotide encoding a polypeptide as defined above; (c)a terminationsequence.

Accordingly, in another aspect the present invention provides arecombinant, purified, or isolated polynucleotide comprising thesequence of SEQ ID NO:2 or a variant thereof encoding either thepolypeptide comprising the amino acid sequence of SEQ ID NO:l or afunctionally equivalent fragment of said polynucleotide.

Accordingly, in another aspect the present invention provides arecombinant, purified or isolated polynucleotide with a nucleotidesequence complementary to the polynucleotide defined above.

Accordingly, in another aspect the present invention provides one ormore oligonucleotide or polynucleotide primers capable of amplifying apolynucleotide which encodes a polypeptide as defined above in aPolymerase Chain Reaction or other polynucleotide amplification method.

Accordingly, in another aspect the present invention provides one ormore oligonucleotide or polynucleotide primers capable of amplifying apolynucleotide which encodes a polypeptide which has a) the amino acidsequence set forth in FIG. 1 (SEQ ID NO:1), or b) a functionallyequivalent variant which has greater than 77% amino acid sequenceidentity with said polypeptide, or c) a functionally equivalent fragmentof a polypeptide defined in a) or b), in a Polymeiase Chain Reaction orother polynucleotide amplification method.

Accordingly, in another aspect the present invention provides a purifiedor isolated antibody capable of binding a polypeptide as defined above.The antibody may be monoclonal or polyclonal or a recombinant antibody.

In a related aspect, antibodies used in methods of the invention may bepresent in an antiserum.

Accordingly, in another aspect the present invention provides anyisolated or purified antibody capable of binding a polypeptide which hasa) the amino acid sequence set forth in FIG. 1 (SEQ ID NO:1), or b) afunctionally equivalent variant which has greater than 77% amino acidsequence identity with said polypeptide, or c) a functionally equivalentfragment of a polypeptide defined in a) or b).

Accordingly, in another aspect the present invention provides acomposition comprising a polypeptide or functionally equivalent variantor fragment thereof of the invention together with an acceptablediluent, carrier, excipient, or adjuvant, said polypeptide being presentin an amount sufficient to generate a protective immune response toMycobacterium avium subspecies paratuberculosis infection, saidcomposition suitable for use as a vaccine.

Accordingly, in another aspect the present invention provides acomposition which comprises a polypeptide which has a) the amino acidsequence set forth in FIG. 1 (SEQ ID NO:1), or b) a functionallyequivalent variant which has greater than 77% amino acid sequenceidentity with said polypeptide, or c) a functionally equivalent fragmentof a polypeptide defined in a) or b).

Accordingly, in another aspect the present invention provides adiagnostic composition comprising a polypeptide of the invention whereinthe composition is a component in an assay.

Accordingly, in another aspect the present invention provides adiagnostic composition as defined above wherein the composition is acomponent is an assay and wherein the assay is capable of detecting thepresence of Mycobacterium avium subspecies paratuberculosis.

Accordingly, in another aspect the present invention provides adiagnostic composition as defined above wherein the composition is acomponent is an assay and wherein the assay is capable of detecting thepresence of Mycobacterium avium subspecies paratuberculosis at apreclinical phase of Johne's disease.

Accordingly, in another aspect the present invention provides adiagnostic composition as defined above wherein the composition is acomponent of an assay kit.

Accordingly, in another aspect the present invention provides acomposition comprising the polynucleotide comprising the sequence setforth in FIG. 2 (SEQ ID NO:2) or a fragment or variant thereof capableof encoding a polypeptide having greater than 77% anmino acid sequenceidentity with the protein encoded by the polynucleotide comprising thesequence set forth in FIG. 2 (SEQ ID NO:2).

Accordingly, in another aspect the present invention provides adiagnostic composition comprising a polynucleotide of the inventionwherein the composition is a component in an assay.

Accordingly, in another aspect the present invention provides adiagnostic composition as defined above wherein the composition is acomponent is an assay and wherein the assay is capable of detecting thepresence of Mycobacterium avium subspecies paratuberculosis.

Accordingly, in another aspect the present invention provides adiagnostic composition as defined above wherein the composition is acomponent is an assay and wherein the assay is capable of detecting thepresence of Mycobacterium avium subspecies paratuberculosis at apreclinical phase of Johne's disease.

Accordingly, in another aspect the present invention provides adiagnostic composition defined as above wherein the composition is acomponent of an assay kit.

Accordingly, in another aspect the present invention provides acomposition comprising at least one oligonucleotide or polynucleotideprimer capable of amplifying a polynucleotide which encodes apolypeptide which has the amino acid sequence set forth in FIG. 1 (SEQID NO:1) or a functionally equivalent variant or fragment thereof whichhas greater than 77% amino acid sequence identity with said polypeptide,in a Polymerase Chain Reaction or other polynucleotide amplificationmethod.

Accordingly, in another aspect the present invention provides adiagnostic composition comprising a primer of the invention wherein thecomposition is a component in an assay.

Accordingly, in another aspect the present invention provides adiagnostic composition as defined above wherein the composition is acomponent is an assay and wherein the assay is capable of detecting thepresence of Mycobacterium avium subspecies paratuberculosis.

Accordingly, in another aspect the present invention provides adiagnostic composition as defined above wherein the composition is acomponent is an assay and wherein the assay is capable of detecting thepresence of Mycobacterium avium subspecies paratuberculosis at apreclinical phase of Johne's disease.

Accordingly, in another aspect the present invention provides adiagnostic composition as defined above wherein the composition is acomponent of an assay kit.

Accordingly, in another aspect the present invention provides acomposition comprising an antibody capable of binding a polypeptidewhich has a) the amino acid sequence set forth in FIG. 1 (SEQ ID NO:1),or b) a functionally equivalent variant which has greater than 77% aminoacid sequence identity with said polypeptide, or c) a functionallyequivalent fragment of a polypeptide defined in a) or b).

Accordingly, in another aspect the present invention provides adiagnostic composition comprising an antibody as defined above whereinthe composition is a component in an assay.

Accordingly, in another aspect the present invention provides adiagnostic composition as defined above wherein the composition is acomponent is an assay and wherein the assay is capable of detecting thepresence of Mycobacterium avium subspecies paratuberculosis.

Accordingly, in another aspect the present invention provides adiagnostic composition defined as above wherein the composition is acomponent is an assay and wherein the assay is capable of detecting thepresence of Mycobacterium avium subspecies paratuberculosis at apreclinical phase of Johne's disease.

Accordingly, in another aspect the present invention provides adiagnostic composition as defined above wherein the composition is acomponent of an assay kit.

Accordingly, in another aspect the present invention provides a methodof detecting Johne's disease including preclinical Johne's disease in ananimal comprising contacting a sample with a polypeptide of theinvention or a composition comprising a polypeptide of the invention anddetecting a response indicative of the presence of Mycobacterium atriumsubspecies paratuberculosis.

Accordingly, in another aspect the present invention provides a methodwhich comprises contacting an animal or a sample from an animal with apolypeptide of the invention or a composition comprising a polypeptideof the invention and detecting a delayed-type hypersensitivity response.

Accordingly, in another aspect the present invention provides a methodwhich comprises contacting a sample with a protein of the invention or acomposition comprising a polypeptide of the invention and detecting inthe sample the presence of antibodies that bind a polypeptide of theinvention.

Accordingly, in another aspect the present invention provides a methodwherein the detection of the presence of antibodies is by immunoassay.

Accordingly, in another aspect the present invention provides a methodwherein the detection of the presence of antibodies is by ELISA,radioimmunoassay-assay, or Western Blot.

Accordingly, in another aspect the present invention provides a methodof detecting Johne's disease including preclinical Johne's disease in ananimal comprising contacting a sample with antibody that binds apolypeptide of the invention or a composition comprising said antibodyand detecting the presence of said bound antibody.

Accordingly, in another aspect the present invention provides a methodwherein the presence of bound antibody is determined by immunoassay.

Accordingly, in another aspect the present invention provides a methodwherein the presence of bound antibody and/or ligand is determined byELISA, radioimmunoassay, or Western blot

Accordingly, in another aspect the present invention provides a methodwhich is capable of detecting the presence of Mycobacterium aviumsubspecies paratuberculosis at a preclinical phase of Johne's disease.

Accordingly, in another aspect the present invention provides a methodof detecting Johne's disease including preclinical Johne's disease in ananimal comprising contacting a sample with a composition comprising ofat least one oligonucleotide or polynucleotide primers capable ofamplifying a polynucleotide which encodes a polypeptide of the inventionin a Polymerase Chain Reaction or other polynucleotide amplificationmethod.

Accordingly, in another aspect the present invention provides a methodof detecting Johne's disease including preclinical Johne's disease in ananimal comprising contacting a sample with a composition comprising apolynucleotide capable of binding to a polynucleotide which encodes apolypeptide of the invention, and detecting said binding.

Accordingly, in another aspect the present invention provides a methodwherein said polynucleotide capable of binding to a polynucleotide whichencodes a polypeptide of the invention is detectably labeled.

Accordingly, in another aspect the present invention provides a methodwherein said detectable label is a radioisotope or fluorescent tag.

Preferably, in any of the methods described above, said animal is aruminant. More preferably, said animal is a sheep.

Accordingly, in another aspect the present invention provides a methodof prophylactically or therapeutically treating an animal againstJohne's disease.

Accordingly, in another aspect the present invention provides a methodwhich comprises administering to an animal a polypeptide of theinvention or functional variant or fragment thereof and/or aprophylactic or therapeutic composition comprising said polypeptide ofthe invention or functional variant or fragment thereof, to engender inthe animal a protective immunological response.

Accordingly, in another aspect the present invention provides a methodwhich comprises administering to an animal a polypeptide of theinvention or functional variant or fragment thereof and/or a therapeuticcomposition comprising said polypeptide of the invention or functionalvariant or fragment thereof, to engender in the animal a protectiveresponse.

Accordingly, in another aspect the present invention provides a methodwherein the prophylactic method comprises administering to said animal avaccine composition comprising an acceptable diluent, carrier,excipient, or adjuvant, in addition to an immunologically protectiveamount of a polypeptide of the invention or functionally equivalentvariant or fragment thereof, in an amount sufficient to produce aprotective response.

Accordingly, in another aspect the present invention provides a methodwherein said administration is performed on a single occasion.

Accordingly, in another aspect the present invention provides a methodwherein said administration is performed on more than one occasion.

Preferably, the amount of polypeptide administered lies in the range of0.1-1000 μg/kg.

Preferably, the amount of polypeptide administered lies in the range of5-5000μg/kg

Preferably, in any of the methods described above said animal is aruminant. More preferably, said animal is a sheep.

Accordingly, in another aspect the present invention provides a kit foruse in detecting the presence of Mycobacterium avium subspeciesparatuberculosis comprising at least two of the following: a) apolypeptide of the invention; b) an antibody that binds saidpolypeptide, and c) a reagent for determining antigen-antibody binding.

Accordingly, in another aspect the present invention provides a kitcomprising at least one oligonucleotide or polynucleotide primerscapable of amplifying a polynucleotide which encodes a polypeptide ofthe invention, and optionally a polynucleotide which encodes apolypeptide of the invention, for use in detecting the presence ofMycobacterium avium subspecies paratuberculosis.

Accordingly, in another aspect the present invention provides a kitwhich is capable of detecting the presence of Mycobacterium aviumsubspecies paratuberculosis at a preclinical phase of Johne's disease.

Accordingly, in another aspect the present invention provides acell-line, vector, or construct which includes a polynucleotide capableof encoding a polypeptide of the invention or functional variant orfragment thereof.

Accordingly, in another aspect the present invention provides a hostcell incorporating a vector or construct of the invention capable ofexpressing a polypeptide of the invention or functional variant orfragment thereof

Accordingly, in another aspect the present invention provides a hostcell wherein said vector exists within the host cell as a plasmid.

Accordingly, in another aspect the present invention provides a hostcell wherein said vector is integrated into the genome of the host cell.

Accordingly, in another aspect the present invention provides a methodof transforming a cell with a polynucleotide capable of encoding apolypeptide of the invention or functionally equivalent variant orfragment thereof.

DESCRIPTION OF THE DRAWINGS

While the present invention is broadly as defined above, it alsoincludes embodiments of which the following description providesexamples. In particular, a better understanding of the present inventionwill be gained through reference to the accompanying drawings in which:

FIG. 1 depicts the amino acid sequence of the protein (SEQ ID NO. 1) asinferred from the nucleotide sequence partially obtained from clonepTB-16, and subsequently amplified from the genome of M. ptb ATCC 53950and sequenced. The amino acids comprising the signal sequence areunderlined.

FIG. 2 depicts the nucleotide sequence (SEQ ID NO. 2) of the 705 basepair gene that encodes the protein. The nucleic acids encoding the aminoacids comprising the signal sequence are underlined.

FIG. 3 shows the expression of the recombinant his-tagged protein fromM. smegmatis. Protein was prepared from sonicated cells harbouringplasmid pMIP-p22 or pMIP 12. Resulting soluble and insoluble fractionswere electrophoresed in 15% SDS-PAGE gels. (a) Coomassie Blue stainedgel. (b) Western blot analysis using 1:500 anti-histidine×6 PODconjugated antibody. Lane M, molecular weight standard; lane 1, pMIP12insoluble; lane 2, pMIP12 soluble; lane 3, pMIP-p22 insoluble; lane 4,pMIP-p22 soluble. Lanes 5 to 8 contain protein fractions collected fromNi⁺²-affinity chromatography of the soluble fraction of cells harbouringpMP-p22. Lane 5, unbound protein; lane 6, 40 mM imidazole elution; lane7,250 mM imidazole elution; lane 8, 1 M imidazole elution. Recombinanthistidine-tagged protein is indicated by the arrows.

FIG. 4 shows detection of antibody to the protein of the invention insheep vaccinated with Neoparasec, such that of 11 sheep vaccinated withthe live attenuated Neoparasec vaccine, 10 produced a strong antibodyresponse to the protein. Western blots of recombinant protein wereindividually incubated with 1:1,000 dilution of sera Anti-sheep IgG PODconjugated antibody was used at 1:20,000. (a) Mob 1 sheep. Lane M,molecular weight standard (kDa); lanes 1 to 6, pooled three and sevenmonth post-vaccination sera from animals 124, 127, 129, 131, 132 and136, respectively. Lanes 7 to 12, pooled one and two monthpre-vaccination sera from the same animals. Lane 13, anti-histidine×6POD conjugated antibody control. (b) Mob 2 sheep. Lane M, molecularweight standard (kDa); lanes 1 to 5, post-vaccination sera from animals507, 578, 587 (three month post-vaccination), 598* (two monthpost-vaccination), and 560* (one month post-vaccination), respectively.Lanes 6 to 10, one month pre-vaccination sera from the same animals,respectively. Lanes 11 to 14, sera from unvaccinated animals 599, 569,527 and 538, respectively, taken at the equivalent of three monthspost-vaccination. * died after this time

FIG. 5 shows the detection of antibody to the protein of the inventionin individual sheep from a naturally infected flock. Western blots ofrecombinant protein were individually incubated with 1:500 dilution ofserum. Anti-sheep IgG POD conjugated antibody was used at 1:40,000dilution. Blots were developed by chemiluminescent detection. Lane M,molecular weight standard (kDa); lanes 1 to 14, sheep number 48, 44,40,36, 6,13, 2, 23, 51, 32, 25, 27, 26 and 43, respectively. * animalsdiagnosed with Johne's disease.

FIG. 6 shows the detection of antibody to the protein of the inventionin naturally infected cattle. Western blots of recombinant protein wereindividually incubated with 1:500 dilution of serum. Anti-bovine IgG PODconjugated antibody was used at 1:20,000 dilution. Blots were developedby chemiluminescent detection. Lanes M, molecular weight standard (kDa);lane 1 anti-histidine×6 POD conjugated antibody control; lanes 2 to 14,preclinical cattle which tested positive on at least one faecal culture(animal 242, 275, 144, 327, 181, 115, 34, 49, 517, 168, 58, 68,respectively); lanes 15 and 16, clinically affected (symptomatic) cattle(animal 27 and 25); lanes 17 to 22, cattle that were negative on allfaecal culture and serum ELISA tests (animal 211, 132, 193, 97, 174,53). The position of the protein of the invention is indicated on bothsides by arrows. See Table 1 for ELISA and faecal culture results.

FIG. 7 shows IFN-γ induction using Ni⁺²-affinity-enriched protein inNeoparasec-vaccinated sheep blood. Whole blood was incubated with 12.5μg/ml Avian PPD in duplicate wells and 2.6 μg/ml, 0.64 μg/ml and 0.32μg/ml Ni⁺²-affinity enriched protein, in single wells. IFN-γ assays wereperformed as described. Results were expressed as “corrected” absorbanceat 450 nm. For Avian PPD, this was defined as the average A₄₅₀ nm of theAvian PPD-stimulated wells minus the average A450 nn of the PBS controlwells for that animal. For each protein concentration, this was definedas the A₄₅₀ nm of the protein-stimulated well minus the average A₄₅₀ nmof the PBS control wells for that animal. There was a significantdifference (p<0.01) in the IFN-γ responses to the protein of theinvention at all three concentrations between the Neoparasec vaccinatedand unvaccinated group.

FIG. 8 shows IFN-γ induction by purified recombinant protein inNeoparasec-vaccinated sheep blood. Whole blood was incubated induplicate wells with 12.5 μg/ml Johnin PPD and 1 μg/ml size-exclusionpurified protein of the invention. To demonstrate aconcentration-dependent response, Neoparasec vaccinated animals 124, 127and 129 and unvaccinated animals 128, 133 and 137 were similarly testedwith 5 μg/ml purified protein. PBS was included as a negative control induplicate wells. IFN-γ assays were performed as described. Results wereexpressed as “corrected” absorbance at 450 mn, defined as the averageA_(450nm) of the stimulated wells minus the average A_(450nm) of the PBScontrol wells for that animal.

FIG. 9 shows detection of antibody to the protein of the invention fromsheep vaccinated with M. ptb strain 316F culture filtrate. Western blotsof recombinant protein were individually incubated with 1:500 dilutionof serum as described. Anti-sheep IgG POD conjugated antibody was usedat 1:40,000 dilution. Blots were developed by chemiluminescentdetection. Lane M molecular weight standard (kDa); lanes 1 to 5, onemonth post-vaccination animals 571, 513, 514, 512 and 551, respectively;lanes 6 to 10, pre-vaccination, same animals.

FIG. 10 shows western blot detection of rabbit antibody raised to theprotein of the invention Ni⁺²-affinity enriched recombinant protein waselectrophoresed in SDS-PAGE gels and transferred to PVDF membranes forsubsequent immnunodetections with the following sera: lane 1, serum fromrabbits immunized with the protein of the invention (1:1,000); lane 2,naïve rabbit serum (1:1,000); lane 3, control anti-histidine×6 PODconjugated antibody (1:500). Lane M, molecular weight standard (kDa).Secondary anti-rabbit IgG POD conjugated antibody was used at 1:20,000.Blots were developed using chemiluminescent detection.

FIG. 11 shows detection of native protein of the invention in Westernblots of M. ptb strain 316F cell fractions and comparison to recombinantprotein using rabbit antibody raised to the protein of the invention.(a) M. ptb cell fractions. Lane M, molecular weight standard (krDa);lane 2, 10 μl (0.5 mg) of 200 fold concentrated culture filtrate; lane3, 10 μl of equivalent 200 fold concentrated soluble cell lysatefraction; lane 4, 10 μl of equivalent 200 fold concentrated insolublecell fraction. (b) Native protein in M. ptb culture filtrate andrecombinant protein from M. smegmatis. Lane M, molecular weight standard(kDa); lane 1, 5 μg culture filtrate; lane 2, 5 μg culture media only;lane 3, 1 μg Ni⁺²-affinity purified recombinant protein from M.smegmatis lysate; lane 4, 0.1 μg Ni⁺²-affinity purified recombinantprotein from M. smegmatis lysate, incubated with 1:500 dilutionanti-histidine×6 POD conjugated antibody (control). Rabbit sera againstthe protein of the invention was used at 1:1,000 dilution. Secondaryanti-rabbit IgG POD conjugated antibody was used at 1:20,000 dilution.Blots were developed using chemiluminescent detection as described.Arrows indicate the location of the protein of the invention.

FIG. 12 shows PCR amplification of the gene encoding the protein of theinvention from 13 isolates of M. ptb. PCR reactions were carried outusing purified DNA as template and primer annealing at 62° C. Samples of5 μl were electrophoresed in 1% agarose gels, stained with ethidiumbromide and photographed under UV light Lane M, DNA size standard; lanes1 to 3, New Zealand farmed deer isolates type C1; lanes 4 to 6, NewZealand sheep isolates type S1; lane 7, New Zealand sheep isolate typeS5; lanes 8 and 9, South African sheep isolates type I; lane 10, NewZealand cattle isolate type C1; lane 11, Faeroe Islands sheep isolatetype S2. The DNA from the five IS900-typed strains were gifted by Dr.Desmond Collins, AgResearch, Wallaceville Animal Research Centre, NewZealand. Lane 12, ATCC 53950; lane 13, strain 316F; lane 14, negativecontrol (water).

FIG. 13 shows PCR amplification from 22 mycobacterial strains usingprimers designed to the ORF encoding the protein of the invention. PCRreactions were carried out using primers 1pp-27fBam and 1pp27-rKpn attwo annealing temperatures. Samples of 5 μl were electrophoresed on 1%agarose gels, stained with ethidium bromide and photographed under UVlight Simultaneous amplification of the 16S rRNA gene was carried outfor each sample as a positive control (a single representative isshown). (a) 55° C. annealing temperature. (b) 62° C. annealingtemperature. Lane M, DNA size standard; lane 1, M. ptb ATCC 53950; lane2, M. ptb 316F; lane 3, M. intracellularae; lane 4, M. scrofulaceum;lane 5, M. fortuitum; lane 6, M. tenrae; lane 7, M. phlei; lane 8, M.smegmatis; lane 9, M. kansasii; lane 10, M. gordonae; lane 11, M.marimum; lane 12, M. bovis 35746: lane 13, M. bovis 19210; lane 14, M.bovis KML; lane 15, M. bovis 35725; lane 16, M. bovis 35726; lane 17, M.bovis canine isolate; lane 18, BCG (Pasteur); lane 19, BCG (Glaxo); lane20, BCG (Japan); lane 21, M. tuberculosis H₃₇Ra; lane 22, M.tuberculosis fur seal isolate; lane 23, negative control (water); lane24, representative positive control 16S rRNA from M. ptb ATCC 53950. The725 base pair PCR product is indicated by the white arrow. The red arrowshows a weak 725 base pair product produced in the M. tuberculosiscomplex at 55° C.

FIG. 14 shows Southern blot analyses from genomic DNA of 13mycobacterial strains using a probe to the gene encoding the protein ofthe invention. Approximately 1 μg of each DNA was digested with BamHI,electrophoresed and transferred to nylon membranes as described. ProbeDNA was labeled by incorporation of DIG-dUTP during PCR of the ORFencoding the protein of the invention. The blot was developed withCDP-star and exposed to film for 2 h. Lane 1, M. bovis BCG (Pasteur);lane 2, M. tuberculosis H₃₇Ra; lane 3, M. bovis (KML); lane 4, M.intracellularae; lane 5, M. ptb 316F; lane 6, M. scrofulaceum; lane 7;M. gordonae; lane 8, M. konsasii; lane 9, M. phlei; lane 10, M. narinum;lane 11, M. terrae; lane 12, M. fortuitum; lane 13, M. ptb ATCC 53950.

FIG. 15 depicts SDS-PAGE analysis showing (lane 1) concentrated proteinof the invention from one of the batches used to prepare the recombinantprotein of the invention vaccine used in this trial, and (lane 2) themolecular weights standard.

FIG. 16 depicts protein of the invention-elicited IFN-γ production inblood samples from the 5 sheep vaccinated with the protein of theinvention, as compared with that from 2 of the Neoparasec vaccinatedsheep, and two of the non-vaccinated sheep. The columns at the far rightreflect the data means. Neo=Neoparasec vaccinated sheep,unvac=non-vaccinated sheep, and protein=protein of theinvention-vaccinated sheep.

FIG. 17 shows a Western blot of recombinant protein of the invention,using for primary detection: A) serum from unvaccinated sheep; B) serumfrom sheep vaccinated with recombinant protein of the invention; C)serum from Neoparasec vaccinated sheep. The numbers represent theidentification numbers of the individual sheep from which the serum wasdrawn.

FIG. 18 shows detection of antibodies specific to the protein of theinvention in serum (diluted 1:200) 5 weeks post vaccination.

FIG. 19 shows detection of antibodies specific to the protein of theinvention in serum (diluted 1:800) 5 weeks post vaccination.

DESCRIPTION OF THE INVENTION

As broadly outlined above, in one aspect the invention provides a novelprotein which has the amino acid sequence as set forth in FIG. 1(SEQ IDNO. 1).

The molecular weight of the protein is 22 kfDa, as assessed by SDS-PAGE.Amino acid sequence analysis suggests the protein is a lipoprotein. Theprotein can be detected in the culture filtrate of M. ptb, suggesting itis a weakly associated envelope protein.

The protein of the invention can include its entire native amino acidsequence or can include only parts of that sequence where such partsconstitute fragments which remain biologically active (activefragments). Such activity will normally be as an immunogen, but is notrestricted to this activity.

Analogs of the protein and of its encoding polynucleotides are alsowithin the scope of the present invention. Such analogs includefunctionally equivalent variants of the protein and of thepolynucleotides described below.

The invention also includes within its scope functionally equivalentvariants of the protein of FIG. 1 (SEQ ID NO. 1).

The phrase “frictionally equivalent variants” recognises that it ispossible to vary the amino acid sequence of a protein while retainingsubstantially equivalent functionality. For example, a protein can beconsidered a functional equivalent of another protein for a specificfunction if the equivalent peptide is immunologically cross-reactivewith and has at least substantially the same function as the originalprotein.

The functionally equivalent protein need not be the same size as theoriginal. The equivalent can be, for example, a fragment of the protein,a fusion of the protein with another protein or carrier, or a fusion ofa fragment with additional amino acids. Active fragments may be obtainedby deletion of one or more amino acid residues of full-length protein ofthe invention. It is also possible to substitute amino acids in asequence with equivalent amino acids using conventional techniques.Groups of amino acids normally held to be equivalent are:

-   -   (a) Ala, Ser, Thr, Pro, Gly;    -   (b) Asn, Asp, Glu, Gln;    -   (c) His, Arg, Lys;    -   (d) Met, Leu, Ile, Val; and    -   (e) Phe, Tyr, Trp.

That equivalent may, for example, be a fragment of the proteincontaining from 8 to 50 amino acids, a substitution, addition ordeletion mutant of the protein, or a fusion of the protein or a fragmentor a mutant with other amino acids.

It is of course also possible (and expressly contemplated) that thebioactive peptides be or include any one of the octapeptides,nonapeptides, or decapeptides from the sequence.

Peptides which are, or include an octapeptide, nonapeptide ordecapeptide from the protein of the invention from M. ptb ATCC 53950 arepreferred.

The practice of the present invention will employ, unless otherwiseindicated, conventional techniques of molecular biology (includingrecombinant techniques), microbiology, cell biology, biochemistry andimmunology, which are within the skill of the art. Such techniques areexplained fully in the literature, such as, Molecular Cloning: ALaboratory Manual, second edition (Sambrook et al., 1989);Oligonucleotide Synthesis (M. J. Gait, ed., 1984); Animal Cell Culture(R. I. Freshney, ed., 1987); Handbook of Experimental Immunology (D. M.Weir & C. C. Blackwell, eds.); Gene Transfer Vectors for Mammalian Cells(J. M. Miller & M. P. Calos, eds., 1987); Current Protocols in MolecularBiology (F. M. Ausubel et al., eds., 1987); PCR: The Polymerase ChainReaction, (Mullis et al., eds., 1994); Current Protocols in Immunology(J. E. Coligan et al., eds., 1991); The Immunoassay Handbook (DavidWild, ed., Stockton Press NY, 1994); Antibodies: A Laboratory Manual(Harlow et al., eds., 1987); and Methods of Immunological Analysis (R.Masseyeff, W. H. Albert, and N. A. Staines, eds., Weinheim: V C HVerlags gesellschaft mbH, 1993).

Polypeptide sequences may be aligned, and percentage of identical aminoacids in a specified region may be determined against another sequence,using computer algorithms that are publicly available. The similarity ofpolypeptide sequences may be examined using the BLASTP algorithnl BLASTPsoftware is available on the NCBI anonymous FTP server(ftp://ncbi.nlm.nih.gov) under /blastlexecutables/. The use of the BLASTfamily of algorithms, including BLASTP, is described at NCBI's websiteat URL http://www.nobi.nlm.nih.gov/BLAST/newblast.html and in thepublication of Altschul, Stephen F., et al. (1997), “Gapped BLAST andPSI-BLAST: a new generation of protein database search programs”,Nucleic Acids Res. 25:3389-34023.

Polypeptides of the invention also include homologous polypeptideshaving an amino acid sequence with at least 77% identity to the proteinof the invention, preferably at least about 80% identity, morepreferably at least about 90% identity, as well as those polypeptideshaving an amino acid sequence at least about 95%, 96%, 97%, 98%, and 99%identical to the protein.

Variants of the protein may be prepared using standard mutagenesistechniques such as oligonucleotide-directed site specific mutagenesis.

The invention also encompasses active fragments with bioactivefunctionality of the protein. Such active fragments may be obtained bydeletion of one or more amino acid residues of full-length protein.Active fragments or portions of the protein may be ascertained bystepwise deletions of amino acid residues, from the N-terminal end orthe C-terminal end or from within the polypeptide. If an amino acid isdeleted and the bioactivity of the protein is not substantially reduced,then the amino acid may not comprise a portion of the active fragment.Further, polypeptides comprising an active fragment of the protein orits analog(s) are also encompassed in the invention.

A protein of the invention, its active fragments or other variants maybe generated by synthetic or recombinant means (i.e. single or fusionpolypeptides). Polypeptides, especially shorter polypeptides up to about50 amino acids, are conveniently made by chemical synthesis usingtechniques well known to those of ordinary skill in the art. Forexample, to be prepared synthetically, the protein or its activefragments or other variants may be synthesised using any of thecommercially available solid phase techniques such as the Merryfieldsolid phase synthesis method, where amino acids are sequentially addedto a growing amino acid chain (see Merryfield, J Am. Soc. 85:2146-2149(1963)). Equipment for automative synthesis of peptides is alsocommercially available from suppliers such as Perkin Elmer/AppliedBiosystems, Inc and may be operated according to the manufacturersinstructions.

The protein may also be produced recombinantly by inserting apolynucleotide (usually DNA) sequence that encodes the protein into anexpression vector and expressing the peptide in an appropriate host. Anyof a variety of expression vectors known to those of ordinary skill inthe art may be employed. Expression may be achieved in any appropriatehost cell that has been transformed or transfected with an expressionvector containing a DNA molecule which encodes the recombinant peptides.Suitable host cells include prokaryotes, yeasts and higher eukaryoticcells. Preferably, the host cells employed are Escherichia coli,Mycobacterium smegmatis, yeasts or a mammalian cell line such as COS orCHO, or an insect cell line, such as SF9, using a baculovirus expressionvector. The selection of suitable transcription and translation controlelements, such as promoters, terminators, enhancers, ribosome-bindingsites, termination signals and the like, for expression in the host cellis well known in the art. For example, in a preferred embodiment, theprotein of the invention may be expressed in E. coli utilizing a highlevel expression system under the control of an inducible promoter, suchas any of the pET (Novagen) vectors, which utilize the T7 promoter. TheDNA sequence expressed in this matter may encode the naturally occurringprotein, fragments of the naturally occurring protein or variantsthereof.

DNA sequences encoding the protein or fragments may be obtained byscreening an appropriate M. ptb cDNA or genomic DNA library for DNAsequences that hybridise to degenerate oligonucleotides derived frompartial amino acid sequences of the protein. Suitable degenerateoligonucleotides may be designed and synthesised by standard techniquesand the screen may be performed as described, for example, in Maniatiset al. Molecular Cloning—A Laboratory Manual, Cold Spring HarbourLaboratories, Cold Spring Haibour, NY (1989). The polymerase chainreaction (PCR) may be employed to isolate a nucleic acid probe fromgenomic DNA, a EDNA or genomic DNA library. The library screen may thenbe performed using the isolated probe.

Variants or homologues of the above polynucleotide sequences also formpart of the present invention. Polynucleotide sequences may be aligned,and percentage of identical nucleotides in a specified region may bedetermined against another sequence, using computer algorithms that arepublicly available. Two exemplary algorithms for aligning andidentifying the similarity of polynucleotide sequences are the BLASTNand FASTA algorithms. The BLASTN software is available on the NCBIanonymous FTP server (ftp://ncbi.nlm.nih.gov) under /blastlexecutables/.The BLASTN algorithm version 2.0.4 [Feb. 24, 1998], set to the defaultparameters described in the documentation and distributed with thealgorithm, is preferred for use in the determination of variantsaccording to the present invention. The use of the BLAST family ofalgorithms, including BLASTN, is described at NCBI's website at URLhttp://www.ncbi.nbm.nih.gov/BLAST/newblast.html and in the publicationof Altschul, Stephen F, et al (1997). “Gapped BLAST and PSI-BLAST: a newgeneration of protein database search programs”, Nucleic Acids Res.25:3389-3402. The computer algorithm FASTA is available on the Internetat the ftp site ftp://ftp.virginia.edupub/fasta/. Version 2.0u4,February 1996, set to the default parameters described in thedocumentation and distributed with the algorithm, is preferred for usein the determination of variants according to the present invention Theuse of the FASTA algorithm is described in the W R Pearson and D. J.Lipman, “Improved Tools for Biological Sequence Analysis,” Proc. Natl.Acad. Sci. USA 85:2444-2448 (1988) and W. R. Pearson, “Rapid andSensitive Sequence Comparison with FASTP and FASTA,” Methods inEnzymology 183:63-98 (1990).

Vectors and/or cells lines which express the protein, a functionallyequivalent variant or active fragment thereof, have utility in their ownright and also form part of the invention.

The invention also includes isolated nucleic acid molecules orpolynucleotides that comprise a polynucleotide sequence as set forth inFIG. 2 (SEQ ID NO. 2) encoding an ORF having at least about 77%identity, preferably 80% identity, preferably at least about 85%identity, more preferably at least about 90% identity, as well as thosepolynucleotides having a nucleic acid sequence at least about 95%, 96%,97%, 98%, or 99%, identical to the protein polynucleotide sequence setforth in FIG. 2 (SEQ ID NO. 2).

Nucleic acid molecules of the invention may be in the form of RNA suchas MnRNA or in the form of DNA, including cDNA, and genomic DNA obtainedby cloning or produced synthetically. The DNA may be double stranded orsingle stranded. Single stranded DNA may be the coding (sense) strand orthe non-coding (anti-sense) strand.

All sequences identified as above qualify as “variants” as that term isused herein.

Variant polynucleotide sequences will generally hybridize to the recitedpolynucleotide sequence under stringent conditions. As used herein,“stringent conditions” refers to prewashing in a solution of 6×SSC, 0.2%SDS; hybridizing at 65° C., 6×SSC, 0.2% SDS overnight; followed by twowashes of 30 minutes each in 1×SSC, 0.1% SDS at 65° C. and two washes of30 minutes each in 0.2×SSC, 0.1% SDS at 65° C. Such hybridizablesequences include those which code for the equivalent protein fromsources (such as other Mycobacterium) other than M. ptb.

While the above synthetic or recombinant approaches can be taken toproduce the protein of the invention, it is however practicable toobtain the protein by isolation from M. avium and/or a subspecies orstrain thereof, or a culture filtrate from M. avium, and/or a subspeciesor strain thereof.

Particularly suitable subspecies of M. avium from which the protein canbe isolated are M. ptb, with M. ptb strain ATCC 53950 being presentlypreferred.

Once obtained, the protein is readily purified if desired. This mayinvolve affinity chromatography in which the immunogenic nature of theprotein is important.

Other approaches to purification (eg. gel-filtration or anion exchangechromatography) can however also be followed. Where the protein orfragment is produced in the form of a fusion protein, the carrierportion of the fusion protein can prove useful in this regard.

Furthermore, if viewed as desirable, additional purification steps canbe employed using approaches which are standard in this art. Theseapproaches are fully able to deliver a highly pure preparation of theprotein. Preferably, the protein preparation comprises at least about50% by weight of the protein, preferably at least about 80%, preferablyat least about 90%, and more preferably at least about 95% by weight ofthe protein.

The purification procedure will of course depend on the degree of purityrequired for the use to which the protein or fragment is to be put.

Once obtained, the protein and/or its active fragments and/or itsfunctionally equivalent variants can be formulated into a compositionThe composition can be, for example, a therapeutic composition forapplication as a veterinary pharmaceutical, a vaccine, or a diagnosticcomposition. For these purposes it is generally preferred that theprotein be present in a pure or substantially pure form.

Again, standard approaches can be taken in formulating such compositions(see for example, Remington's Pharmaceutical Sciences, 18^(th) Edition,Mack Publishing (1990)).

In one embodiment, the protein, its functionally equivalent variants oractive fragments are employed as antigens to elicit a host-protectiveresponse in an animal. It will be appreciated that in accordance withthis embodiment, the antigen of the invention can be administered eitheralone or in the form of a composition including a vaccine preparationcomprising the antigen as the active ingredient together with apharmaceutically acceptable diluent, carrier, excipient, or adjuvant.

Examples of suitable adjuvants known to those skilled in the art aresaponins (or derivative or related material), muramyl dipeptide,trebalose dimycollate, Freund's complete adjuvant, Freund's incompleteadjuvant, other water-in-oil emulsions, double emulsions, dextran,diethylaminoethyl-dextran, potassium alum, aluminium phosphate,aluminium hydroxide, bentonite, zmosan, polyelectrolytes, retinal,calcium phosphate, protamine, sarcosine, glycerol, sorbitol, propyleneglycol, fixed oils and synthetic esters of higher fatty acids. Saponinsare generally preferred.

The antigen of the invention may also be treated in any conventional wayto enhance its stability or to conserve or potentiate its immunogenicefficacy. For example, the antigen may be treated with a suitableinhibitor, modifier, crosslinker, or denaturant in such a way as toenhance its immtmogenicity.

In addition, the antigen can be administered in combination with othertherapeutic agents.

It is also possible to include an additional immunogen in the solutionor composition for administration as a vaccine. Such an immunogen willgenerally be a TH1 type immune response inducing substance.

An immunogenic composition including a vaccine of the invention can beadministered to the animal by any of those methods known in the art.However, the preferred mode of administration is parenteral. The term“parenteral” is used herein to mean intravenous, intramuscular,intradermal, and subcutaneous injection. Most conveniently, theadministration is by subcutaneous injection.

Despite the preference for parenteral administration, it is by no meansintended to exclude administration of the immunogenic composition inother forms.

Administration of the immunogenic composition of the invention may beconveniently carried out at a single time point. Alternatively, theimmunogenic composition may be administered more than once.

The amount of composition administered to the animal to be treated willdepend on the type, size and body weight of the animal as well as on theimmunogenicity of the immunogenic composition. Conveniently, in the caseof a vaccine, the vaccine is formulated such that relatively smallvolumes of vaccine (1 to 5 mL) are sufficient to protect the animal towhich they are administered. Similarly, where the immunogen of thevaccine is the protein of the invention or a functional variant orfragment thereof as described herein, the vaccine may be formulated sothat a dose comprises between 0.1 μg and 1000 μg immunogen per kg bodyweight of animal, more preferably between 5 μg and 500 μg per kg, morepreferably between 10 μg and 100μg per kg.

The term “animal” as used herein includes ruminants such as cattle,sheep, deer, buffalo, camielids, antelope, and goats. Sheep areparticularly suitable for use with the invention

In addition to the vaccine embodiments described above, it will beunderstood that a live vaccine could also be employed to protect a hostagainst M. ptb infection or Johne's disease. In such a live vaccine, theDNA molecule of the invention encoding the protein, functionallyequivalent variant or active fragment thereof, is incorporated into thegenome of an attenuated carrier organism. A number of carrier organismsare known in the art which are suitable for this purpose with examplesbeing Salmonella and Vaccinia virus.

The live vaccine of this embodiment can be formulated in accordance withmethods known in the art. Similarly, the live vaccine can beadministered parenterally, or by conventional methods to have its effectvia the gastrointestinal tract.

It is well known by those skilled in the art that M. ptb is thecausative pathogen of Johne's disease. A further use of the protein ofthe invention, its functionally equivalent variant or active fragmentthereof, is in the field of diagnosis of M. ptb infection and/or Johne'sdisease. More particularly, it will be understood by those personsskilled in the art that the protein, functionally equivalent variant oractive fragment thereof, may be employed as highly specific diagnosticreagents for detection of the presence of M. ptb in an animal suspectedof harbouring the disease. The diagnostic procedure employed to detectM. ptb and/or Johne's disease may involve the detection of delayed typehypersensitivity to the protein of the invention by skin test or thelike, or may involve an assay of body fluid obtained from the animal.

Similarly, the diagnostic procedure employed to detect M. ptb and/orJohne's disease may involve the use of the protein of the invention as areagent in an IFN-γ EIA test.

It will be understood by those persons skilled in the art that thedetection system selected may employ the protein, functionallyequivalent variant or active fragment thereof, alone as diagnosticreagents.

However, in other systems such diagnostic reagents will include suitablecarrier or marker substances (either chemical, enzymic or radiochemical)in the detection of antibodies by agglutination, radioimmunoassay,fluorescence or enzyme immunoassay techniques. A preferred antibodydetection technique is ELISA.

Another use for the polypeptides of the invention is the generation ofantibodies, including monoclonal antibodies. Polypeptides of theinvention are used as immunogens to immunize mice. Splenocytes(including lymphocytes) are obtained from the immunized mice. Hybridomasare prepared from the lymphocytes and immortalized myeloma cells usingthe general somatic cell hybridization technique of Kohler, B. andMilstein, C. Nature 256:495-497 (1975). Other modified methods, forexample by Buck, D. W., et al., In Vitro, 18:377-381 (1982) may also beused. Available myeloma lines, including but not limited to X63-Ag8.653and those from the Salk Institute, Cell Distribution Center, San Diego,Calif., USA, may be used in the hybridization. The technique involvesfusing the myeloma cells and lymphoid cells using a fusogen such aspolyethylene glycol, or by electrical means well known to those skilledin the art. After the fusion, the cells are separated from the fusionmedium and grown in a selective growth medium, such as HAT medium, toeliminate unhybridized parent cells. Any of the media described herein,supplemented with or without serium, can be used for culturinghybridomas that secrete monoclonal antibodies. As another alternative tothe cell fusion technique, EBV immortalized B cells are used to producethe monoclonal antibodies of the subject invention. The hybridomas areexpanded and subcloned, if desired, and supernatants ale assayed foranti-immunogen activity by conventional immunoassay procedures (e.g.,radioimmunoassay, enzyme immunoassay, or fluorescence immunoassay).

Hybridomas that produce such antibodies may be grown in vitro or in vivousing known procedures. The monoclonal antibodies may be isolated fromthe culture media or body fluids, by conventional immunoglobulinpurification procedures such as ammonium sulfate precipitation, gelelectrophoresis, dialysis, chromatography, and ultrafiltration, ifdesired. Undesired activity if present, can be removed, for example, byrunning the preparation over adsorbants made of the immunogen attachedto a solid phase and eluting or releasing the desired antibodies off theimmunogen.

Polypeptides of the invention may also be used as imminunogens toimiunize other animals (i.e., rats and rabbits) to generate polyclonalantibodies. Methods of producing polygonal antibodies and isolation andpurification thereof is known in the art. See, for example, Harlow andLane (1987). Other suitable techniques for preparing antibodies involvein vitro exposure of lymphocytes to the antigen or alternatively toselection of libraries of antibodies in phage or similar vectors. See,for example Huse et at., 1989.

Also, recombinant antibodies may be produced using procedures known inthe art. See, for example, U.S. Pat. No. 4,816.567.

The antibodies may be used with or without modification. Frequently,antibodies will be labeled by joining, either covalently ornon-covalently a substance which provides a detectable signal. A widevariety of labels and conjugation techniques are known and are reportedextensively in the literature.

Antibodies as above to the protein of the invention can therefore beused to detect or monitor the presence of the protein in an animal or inprotein quantification assays. Further, antibodies to the protein of theinvention can be used to measure levels of the protein in an animal,either at one fixed time point or over a period of time to monitorfluctations in protein levels. Such antibodies can also be used tomeasure levels of the protein in an animal to which drugs, vaccines, orother therapeutic or prophylactic bioactives have been administered. Insuch assays, any convenient immunological format can be employed. Suchformats include immunohistochemical assays, RIA, IRMA and ELISA assays.

The assays can be conducted in relation to any biological fluid whichdoes, or should, contain the protein of the invention. Such fluidsinclude blood, serum, plasma, urine and cerebrospinal fluid.

Antibodies as above to the protein of the invention can therefore beused to detect or monitor the presence of M. ptb and/or Johne's diseasein an animal or in M. ptb quantification assays. Further, suchantibodies can be used to measure levels of M. ptb in an animal, eitherat one fixed time point or over a period of time to monitor fluctationsin M. ptb levels. Such antibodies can also be used to measure levels ofM. ptb in an animal to which drugs, vaccines, or other therapeutic orprophylactic bioactives have been administered. In such assays, anyconvenient immunological format can be employed. Such formats includeimmunohistochemical assays, RIA, IRMA and ELISA assays.

The assays can be conducted in relation to any biological fluid whichdoes, or should, contain the protein of the invention, a functionallyequivalent variant or active fragment thereof, and/or M. ptb. Suchfluids include blood, serum, plasma, urine and cerebrospinal fluid.

Antibodies, monoclonal or polyclonal, against the protein of theinvention may be used for diagnosis or for therapeutic purposes.Antibodies may be used by themselves or attached to a solid substrate,such a column or a plate. Antibodies which are attached to a solidsubstrate may be used for assays, for example ELISA, or as a standard inother assays. Antibodies against the protein of the invention are alsouseful for isolation, purification, and quantitation of the protein ofthe invention.

Those skilled in the art will appreciate that the functional equivalentsof antibodies, such as antibody fragments and/or f_(ab) molecules arealso considered herein.

The antibodies can also be included in assay kits. Such kits cancontain, in addition, a number of optional but conventional components,the selection of which will be routine to the art skilled worker. Suchadditional components will however generally include a protein referencestandard, which may be the protein of the invention itself or ananalog.(such as a fragment).

It will also be appreciated that antibodies such as described above can,in some circumstances also function as antagonists of the protein of theinvention by binding to the protein and partly or completely interferingwith its activity.

Similarly, those skilled in the art will appreciate that other ligandsthat bind the protein of the invention, a functionally equivalentvariant or active fragment thereof, may be used in a fashion analogousto the antibodies to the protein described above.

Aspects of the invention will now be described with reference to thefollowing non-limiting examples.

EXAMPLE 1

To identify potential exported proteins of M. ptb, a library of alkalinephosphatase (phoA) gene fusions was constructed in the vector pJEM11 andexpressed in Escherichia coli and Mycobacterium smegmatis.

Materials and Methods

Extraction of DNA from M. ptb

Approximately 3 mg of lyophilised M. ptb (New Zealand field isolate ATCC53950) was resuspended in 0.6 ml of extraction buffer (100 mM NaCl, 25mM EDTA (pH 8.0), 10 mM Tris.Cl pH 8.0, 0.5%(w/v) SDS) before adding 200μg of proteinase K (Roche Molecular Biochemicals, Germany). The mixturewas incubated at 50° C. for 18 h and then 100 μl of 5 M NaCl and 120 μlof 6.7%(w/v) cetyltriniethylammornium bromide (Aldrich Chemical Company,USA) in 0.5%(w/v) NaCl was added. The digest was mixed with an equalvolume of 25:24:1 phenol:chlorofomi:isoamyl alcohol and centrifiged at15,800×g for 5 min. The aqueous phase was collected and thephenol:chloroform:isoamyl alcohol extraction was repeated, as above. Theaqueous phase was mixed with an equal volume of chloroform andcentrifuged again. The DNA was precipitated with the addition of 1volume of 100% isopropanol to the collected aqueous phase. After 18 h at−20° C., the DNA was pelleted by centrifugation at 15,800×g for 30 minat 4° C. The pellet was washed with 1 ml of 70% ethanol, air dried atroom temperature and resuspended in 100 μl of TE buffer containing 100μg/ml RNAse A (Life Technologies Inc., USA) and incubated for 18 h at37° C. The DNA concentration was calculated based on absorbance at 260nm. To check the condition of the DNA, an 8 μl sample (˜11 μg) waselectrophoresed on a 0.7% agarose gel, stained with ethidium bromide andvisualised under WV light.

Preparation of pJEM11 Vector DNA

pJEM11 plasmid DNA was purified from transformed E. coli DH10B cells.The plasmid DNA was quantitated based on its absorbance at 260 nm.Eleven micrograms of plasmid was digested to completion with 2.5 unitsof BamHI at 37° C. for 2 h and was purified by agarose gel extraction.The resulting digested plasmid DNA was dephosphorylated using 2 units ofalkaline phosphatase (Boehringer Mannheim, Germany) for 1 h at 37° C. toprevent recircularisation of the plasmid. The DNA was then purified byagarose gel extraction.

Partial Digestion of M. ptb Genomic DNA

A partial digest of M. ptb genomic DNA was performed on 2.8 μg of theDNA using 0.05 units Sau3A in a volume of 25 μl at 22° C. From this, 6×4μl samples were removed at 30s intervals and were electrophoresed on a1% agarose gel. DNA ranging in size from approximately 200-3,000 basepairs was extracted from the 1.5 min and 2.0 min digestion lanes fromthe agarose gel. The resulting DNA fragments were eluted in a finalvolume of 50 μl of TE buffer. A 10 μl sample was run on a 1% agarose gelto check recovery.

Ligation of Size Selected M. ptb Genomic DNA and PJEM11 andTransformation into E. coli

Approximately 1 μg of BamHI, alkaline phosphatasetreated pJEM11 vectorDNA and 0.7 μg of Sau 3A partially digested M. ptb DNA were ligatedusing 1.0 unit of T4 DNA ligase in a total volume of 35 μl at roomtemperature for 30 min. The mixture was dialysed and electroporated into100 μl of E. coli DH10B cells. To this, 500 μl of LB broth was added andincubated for 1 h at 37° C. Aliquots of approximately 70 μl each wereplated onto nine LB/kan/BCIP plates and incubated at 37° C. forapproximately 18 h. A representative plate was selected and colonieswere counted on a quarter of the plate to estimate the total number ofresulting transformants. The total number of blue transformants was alsocounted. Blue E. coli colonies were restreaked onto LB/kan/BCIP platesfor confirmation of PhoA⁺ phenotype. Each of these colonies was culturedin LB/kan broth for glycerol storage at −70° C.

Plasmid Isolation From the E. coli Recombinant Library

The recombinant plasmid library was then isolated from E. coli. To eachof the nine plates, 1.6 ml of LB/kan broth was added and the colonieswere resuspended with the aid of a rubber spatula The mixtures from eachplate were transferred to 2 ml microtubes and the plasmid DNA wasextracted using a BRESAspin Plasmid Mini Kit (Bresatec, Australia) withthe modification that all reagent volumes were doubled due to the highconcentration of cells. Each of the nine plasmid preparations was elutedinto 50 μl of TE buffer, for a total volume of 450 μl. The plasmids werestored at −20° C. until used.

Transformation of the Recombinant Plasmids Into M. smegmatis

The recombinant plasmids were then transformed into Mycobacteriumsmegmatis mc²155. Two 10 μl aliquots of the plasmid mixture weredialysed and used to transform two 100 μl aliquots of electrocompetentM. smegmatis cells. To each of the resulting transformations, 500 μl ofLB broth was added and the cells were incubated at 37° C. for 2 h. Fromthis, 80 μl samples were spread onto 15 LB/kan/BCIP plates, which werethen incubated at 37° C. After five days, the plates were transferred to4° C. for a farther 54 days. To estimate the total number of colonies(blue and white), a quadrant of a representative plate was counted. Overthe 59 days, blue colonies were picked daily and designated numerically,as they appeared. These were restreaked onto fresh LB/kan/BCIP platesand grown at 37° C. until they turned blue and then were transferred toglycerol for storage at −70° C.

Sequencing of DNA Inserts Encoding Putative Exported Proteins

To obtain plasmid DNA for sequencing of inserts, the pJEM11 constructswere first transferred from individual M. smegmatis colonies to E. coliDH10B cells. Prior to sequencing, the clones were first screened forpresence of unique inserts by digestion of the plasmids with restrictionendonucleases Kpn I and Apa I, which flank the DNA inserts in pJEM11.Unique inserts were then selected for sequencing.

Results

Construction of an M. ptb pJEM11 Expression Library

In order to identify M. ptb gene sequences encoding exported proteins, alibrary of M. ptb phoA fusions was created in the vector pJEM11 asdescribed above and expressed in E. coili and M. smegmatis.

Since M. smegmatis mc² 155 has a 10⁴ lower rate of transformationefficiency as compared to E. coli (Snapper et al. 1990), the plasmidlibrary was first transformed into E. coli to ensure the highestpossible proportion of constructs could be recovered.

After 18 h at 37° C. a representative E. coli plate had 1,200 colonies.This resulted in an estimated total of 10,800 colonies from nine plates.Of these, 17 colonies were blue. These were designated Eco-1 to Eco-17.Upon a further 18 h storage of the library at 4° C., seven more blue E.coli colonies resulted. These were designated Eco-18 to Eco-24. Thus, atotal of 24 blue E. coli colonies, representing 0.2% of the library wereobtained.

Expression of the Library in M. smegmatis

A sample of the plasmid collection was used to transform M. smegmatis.After three days incubation at 37° C. on LB/kan/BCIP plates, the firstblue M. smegmatis colony appeared and was designated pTB-1. Over thenext two days, a further 45 blue colonies appeared, designated pTB-2 topTB46. The plates were transferred to 4° C. and 473 more blue coloniesappeared over 54 days. A total of 519 blue M. smegmatis clones werecollected. The total number of M. smegmatis colonies was estimated to be60,000, of which 0.9% were blue.

A six-fold increase in the number of colonies was obtained in M.smegmatis (60,000) compared to E. coli (10,800). This was a result ofamplification of the plasmids in E. coli prior to transfer to M.smegmatis. Multiple copies of the plasmids were therefore expected to bepresent in the M. smegmatis library. This expectation was confirmed byanalysis of the pJEM11 plasmid constructs. The average insert size wascalculated from PhoA⁺ constructs analysed by agarose gelelectrophoresis. The plasmids were digested with Apa I and Kpn I, whoserecognition sites flank the Bam HI site in the vector used for cloning.Only unique inserts were included in calculations. From the 128 plasmidsanalysed, the average insert size was 1,700 base pairs. The insertsgenerally ranged in size from 300-3,000 base pairs with a median of1,400 base pairs.

Insert DNA was fully or partially sequenced from 63 individual clones.Of these, 33 were unique in sequence and the rest were redundant. Thepartial gene sequences adjacent to phoa were used to search DNA andprotein databases. Twenty-five of the 33 sequences obtained hadsimilarities to other mycobacteria or Streptomyces genes and includedidentities with a copper/zinc superoxide dismutase, a cutinase, apenicillin-binding protein, a serinethreonine protein kinase and threelipoproteins. One sequence was identical to the previously characterisedgene encoding the M. ptb 34 kDa protein. Seven sequences had nosignificant similarities to any of the sequences on the databases.

N-terminal regions were determined for 21 of the 33 translated openreading frames fused to phoA. These sequences were further analysed forthe presence of conserved signal peptide elements andtransmembrane-spanning regions. Twelve had evidence of signal sequencesand four had predicted transmembrane segments. The remaining five had noevidence of characteristic hydrophobic stretches of amino acids thatmight function as transmembrane segments. Of the twelve sequences withindefinable N-termini, eight had predicted transmembrane-spanningregions.

A putative lipoprotein identified in this study was selected for furtherinvestigations.

EXAMPLE 2

An exported 23 Kda protein, identified as described above, wascharacterised and assessed for its immunoreactivity. The open readingframe encoding the protein was cloned and the protein was expressed inM. smegmatis as a C-terminal polylistidine-tagged recombinant protein asdescribed below.

Materials and Methods

PCR Amplification of the Gene from M. ptb

Genornic DNA extracted from M. ptb ATCC 53950, prepared as describedabove, was used as a template for PCR amplification of the gene encodingthe protein of the invention. Oligonucleotide primers were designed tothe 5′ and 3′ ends of the entire ORF and are shown below. The forwardprimer 1pp27-fBam (SEQ ID NO. 3) was designed to the 5′ end of thepredicted ORF, and the reverse primer 1pp27-rKpn (SEQ ID NO. 4) wasdesigned to the 3′ end of the ORF. The TGA stop codon was omitted toallow read-through to produce the histidine×6 tag coded by the vector.lpp27-fBam 5′ GATGGGATCCATGCAGACCCGCCGCCGCCT lpp27-rKpn 5′TGAGGGTACCCGAGCTCACCGGGGGCTTGG

PCR was done using 1μl of a 1:10 dilution of genomnic DNA template in avolume of 50 μl. The conditions used were an initial melting temperatureof 95° C. for 10 min followed by 35 cycles of 94° C. for 30s, 55° C. for30s, 68° C. for 1 min, and a final extension at 68° C. for 10 min usingplatinum Pfx polymerase, in the presence of 10%(v/v) dimethlysulfoxide.

Cloning of the Open Reading Frame

For expression of the gene encoding the protein of the invention in M.smegmatis, the ORF was cloned into the vector pMIP12. The 725 base pairPCR product was extracted from a 1% TAE agarose gel. The purifiedproduct was eluted in 30 μl of distilled water and a 6 μl sample was runon a 1% agarose gel to check its recovery. The remaining DNA wasdigested with 40 units of KpnI in 40 μl at 37° C. overnight. This wasfollowed by digestion with BamHI in a total volume of 50 μl at 37° C.overnight. The digested product was purified and resuspended in 30 μl ofsterile water using a QIAgen gel extraction kit From this, 6 μl waselectrophoresed on a 1% TAE agarose gel to estimate its concentration.The remainder was used for ligation with pHIP12, as described below.

The vector pMIP12 was isolated from previously transformed E. coli DH10Bcells. Plasmid DNA from two 4 mn cultures grown in LB/kan broth wasresuspended in 100 μl of distilled water. DNA concentration wasquantitated by absorbance at 260 nm. Approximately 2.6 kg of plasmid DNAwas digested with 20 units of KpnI in 20 μl for 4 h at 37° C. To confirmcompletion of digestion, 1 μl was removed and electrophoresed on a 1%TAE agarose gel and photographed. To the remaining 19 μl, 30 units ofBamHI was added and the volume was brought up to 30 μl with water. Themixture was incubated for 18 h at 37° C. The digested vector waselectrophoresed on a 1% low melting point agarose gel (SeaPlaque GTGagarose, FMC BioProducts, Rocldand, Me., USA) in TAE buffer and ethidiumbromide stained for visualisation. The gel slices were cut out in aminimal amount of agarose, transferred to a 1.5 ml microfaige tube andmelted at 68° C. for 10 min. From this mixture, 6 μl was removed andimmediately added to a microfuge tube containing 24 μl of insert DNA,prepared as described above. To this was added unit of T4 DNA ligase ina total volume of 40, and the mixture was incubated at 14° C. overnight.This was dialysed and electroporated into 35 μl of E. coli ElecrtoMaxDH10B cells. To this, 200 μl of LB broth was added and the mixture wasincubated at 37° C. for 1 h. Of this, 50 μl was spread onto a LB/kanplate and incubated overnight at 37° C.

To confirm the presence of the insert, PCR was carried out on five ofthe resulting colonies using the pM[P12 primers BlaF3 and R2 (seebelow), in the presence of Taq polymerase in 20 μl. Eight microlitresfrom each PCR was electrophoresed on a 1% TAE agarose gel and ethidiumbromide stained. The forward primer BlaF3 binds at approximately 150base pairs within the blaF* promoter and is designed to the codingstrand. The reverse primer R2 binds 44 base pairs from the Kpn I siteand is designed to the complementary stiand of the transcriptionalterminator. The expected size of the PCR product for the insert wasapproximately 900 base pairs. BlaF3 5′ TCGCGGGACTACGGTGCC R2 5′TCGAACTCGCCCGATCCC

From a resulting PCR-positive colony, plasmid DNA was extracted from 4ml of broth culture and resuspended in 50 μl of 10 mM Tris (pH 8.0).Eight microlitres of plasmid was digested with 10 units of Kpn I in 10μl at 37° C. overnight. This was followed by digestion with 10 units ofBam HI in a final volume of 25 μl at 37° C. overnight. One microlitrewas electrophoresed on a 1% TAE gel and photographed after ethidiumbromide staining. To confirm the insert identity and the correctinsertion for expression, plasmid was used as template for sequencingusing the primers Bla3 and R2.

Expression and Purification of Recombinant Protein From M. smegmatis

For transfer of pMIP-p22 into M. smegmatis, 1 μl of the plasmid DNA waselectroporated into 20 μl of M smegnatis cells. A 250 μl aliquot ofcells was spread on a LBAcan plate and incubated at 37° C. for threedays. To confirm the presence of pMP-p22, one colony was picked for PCRanalysis using the primers R2 and Bla3 as described above, in a volumeof 100 μl. The resulting 900 base pair product was gel-extracted andsequenced using the same primers.

For preparation of recombinant protein, a single colony ofpMEP-p22-transformed M smegmatis was picked and inoculated into 15 ml ofSauton's broth or modified Middlebrook 7H9 broth containing kan andgrown at 37° C. with vigorous shaking for approximately three days. Thiswas used to inoculate 600 ml of the same media, and the culture wasgrown and harvested and lysates were prepared as described.

The resulting sonicate supernatant was used in Ni⁺²-affinitychromatography, employing four 5 ml columns connected in series andattached to a peristaltic pump. Inidazole concentrations of 40 mM, 250mM and 1 M were used, in the first instance, to determine the elutionprofile of the recombinant protein. Samples from each collected elutionwere used in Western blot analyses to determine where the majority ofthe recombinant protein eluted. Having determined this, the procedurewas repeated using two washes of 100 mM of imidazole prior to the 250 mMelution, to further purify the recombinant protein. Pooled fractionswere concentrated as described, in preparation for Western blotting,IFN-γ assays or size exclusion chromatography.

N-Terminal Protein Sequencing

Automated Edman degradative N-terminal sequencing was carried out byMassey University Protein Sequencing Services using a pulse liquid phasesequenator (Model 476A, Applied Biosystems, USA). This instrumentperforms fully automated sequencing by sequential removal of theN-terminal amino acid as a phenylthiohydantoin-derivative. Derivativeswere separated by HPLC and the data collected and analysed using a Model610A Data Analysis Module (Applied Biosystems, USA). Protein to besequenced was electrophoresed on 15% SDS-PAGE gels and transferred toPVDF membrane as described. Following transfer, the membrane was stainedwith Ponceau S and the desired band(s) were excised and destained indistilled water. Approximately 1 pmol (25 μg for a protein of 25 kDa) ofprotein was used for sequencing.

Results

Expression and Purification of Recombinant Protein from M. smegmatis

In order to increase the likelihood of producing the protein of theinvention in a form resembling that from the original host (M. ptb), itwas expressed in the fast-growing species M. smegmatis. The ORF encodingthe protein of the invention was cloned into the vector pMIP12 and usedto transform M. smegmatis. To aid purification and detection of therecombinant protein, the gene was expressed with a C-terminalhistidine×6 tag from the vector pMIP12. As shown in FIG. 3, therecombinant protein was detected from cell sonicates in both the solubleand insoluble fractions by Western blot analysis using a monoclonalanti-histidine×6 POD conjugated antibody. The recombinant protein wasclearly recognised by the antibody (FIG. 3 b) with no other signalobtained, confirming specificity for the histidine×6 tag. The proteinwas further isolated from the soluble fraction by Ni⁺²-affinitychromatography followed by elution with imidazole as described above.Recombinant protein could be seen in the 250 mM imidazole elution inSDS-PAGE gels with Coomassie Blue staining (see FIG. 3 a). Western blotanalysis showed the 250 mM imidazole elution contained most of theprotein, with a slightly smaller amount present in the 40 nm elution andnone was detected in the 1 M elution. There was a small amount of theprotein still present in the flow-through, indicating that not all ofthe protein was bound to the column. This may be because the column wassaturated with bound protein.

The apparent molecular weight of the recombinant protein from SDS-PAGEwas 23 kDa, which was smaller than the calculated weight of 25.9 kDa forthe full-length recombinant protein, expressed from pMIP12. Thissuggested that the full-length protein may have been cleaved at theN-terminus, as was predicted from its amino acid sequence, and soN-terminal sequencing of the 23 kDa band was carried out, as describedabove. The resulting amino acid sequence obtained, LIAGCS (SEQ ID NO.7), was consistent with an N-terminal cleavage predicted at amino acidposition 19/20 in the native protein by SignalP (see FIG. 1, amino acids20-25). The theoretical size of the mature recombinant product based onthis cleavage was 23.6 kDa and was similar to the apparent molecularmass from SDS-PAGE.

EXAMPLE3

Materials and Methods

Western Blot Analyses of Antibodies in Animal Sera

Western blots were carried out according to methods well known to thoseskilled in the art. For detection of antibody to the protein of theinvention from animal sera, identical amounts of recombinant protein(approximately 0.5 μg) were electrophoresed in individual lanes,alongside a molecular weight standard, on SDS-PAGE gels. The protein wastransferred to PVDF or nitrocellulose membranes and stained with PonceauS to visualise the bands. The lanes were numbered at the top of themembrane and then cut into individual strips.

For immunodetection, single strips were incubated with serum inindividual small glass screw-capped bottles in 2 ml of blocking buffer.The strips remained in the bottles for washing and were then were pooledin plastic trays for incubation with appropriate secondary antibody andwashing. To avoid cross-contamination, strips from differentexperimental groups, eg. unvaccinated and vaccinated, were pooledseparately during this stage. The following secondary POD conjugatedanti-IgG heavy and light chain antibodies were used: goat anti-rabbit (A6154), donkey anti-sheep (A 3415), rabbit anti-bovine (A 7414), (Sigma,USA).

Results

Humoral Immune Responses to the Protein

To investigate immune responses to the protein of the invention,Neoparasec-vaccinated animals were used in the first instance. It washypothesised that vaccinated animals would make an immune response toantigens possessed by the bacteria in the vaccine. In this respect, theymay be similar to infected animals and therefore could be used toevaluate the immunogenicity of the protein of the invention. M. ptbvaccinated cattle and sheep have similarly been used to evaluate variousmycobacterial proteins (Valentin-Weigand & Moriarty, 1992; Koets et al.,1999; 2001).

Serum samples from Neoparasec-vaccinated and naturally infected sheepwere used in individual immunoblot assays to determine their humoralresponse to the protein of the invention. A high level of antibody tothe protein of the invention was produced by 10 of the 11Neoparasec-vaccinated sheep in Western blots analyses, demonstrating theprotein was immunogenic, as shown in FIG. 4. There was a very faint bandproduced by sera from three of the sheep (507, 578 and 560) prior tovaccination and also in two naïve animals (599 and 569). Control serafrom the remaining animals prior to vaccination and from unvaccinatedcontrol animals did not react with the protein (not all are shown).

To investigate if antibody to the protein of the invention was presentin naturally infected animals, Western blots were probed with sera fromsheep and cattle belonging to flocks and herds known to have Johne'sdisease present. Results with sheep sera are shown in FIG. 5. A total offive of 14 sheep had antibody to the protein of the invention. Antibodyto the protein of the invention was detected in two of the five sheepwith confirmed Johne's disease and in two sheep that showed no evidenceof Johne's disease. A weak band was produced with one animal (26) thathad a single suspicious lesion without acid-fast organisms in anexamined lymph node but was not confirmed as having Johne's disease.Immunoblots were repeated several times with consistent results.

FIG. 6 shows the results of Western blot analysis using cattle sera. Asummary of the results for serum ELISA, faecal culture and Western blotanalysis is shown in Table 1. Antibody to the protein of the inventionwas present in sera from 11 of 13 preclinically infected cattle thatwere positive on at least one previous faecal culture. A variety ofstrong and weak bands were produced. Three of the four cows that werepositive on all ELISA and faecal culture tests (24, 144 and 49 but not2) also produced major bands with the protein of the invention. Twopreclinically infected cows (181 and 68) did not have detectableantibody to the protein of the invention and were also negative on thelast ELISA and previous faecal culture. However, other animals withsimilar test results, such as 58 and 34, produced strong bands with theprotein of the invention. Antibody to the protein was present in fourpreclinically infected cows (327, 517, 58, 115) that were negative onall three serwn ELISA tests. Antibody to the protein was also present inboth clinically affected cows (27 ands 25). Cow 27 produced a verystrong band with the protein of the invention. Of the six cows that werenegative on all ELISA tests and faecal cultures, one (53) produced aweak band with the protein of the invention. TABLE 1 Summary of resultsfor detection of M. ptb by serum ELISA, faecal culture and Western blotanalysis Faecal Faecal ELISA culture culture Animal # ELISA 1 ELISA 2 31 2 protein  24 + + + + + +  2 ND + + + + + 275 + − + + + +144 + + + + + + 327 − − − + + + 181 + + − + − − 115 − − − − + +  34 − +− + − +  49 + + + + + + 517 − − − + + + 168 ND − + + + +  58 − − − + − + 68 − − − + − −  27# ND ND ND ND ND +  25* ND ND ND ND ND + 211 − − − −− − 132 − − − − − − 193 − − − − − −  97 − − − − − − 174 − − − − − −  53− − − − − +Serum ELISA and faecal culture were carried out and interpreted aspositive or negative by AgResearch, Wallaceville, Lower Hutt, NewZealand. Sera and faecal culture tests were done in six-monthlyintervals. Sera used for Western blot analysis was from the lastcollection date, corresponding to ELISA 3.ND = not done*Johne's disease diagnosed on clinical signs and gross pathology#Johne's disease diagnosed on clinical signs and acid-fast organisms infaeces

EXAMPLE 4

Materials and Methods

IFN-γ Assays

IFN-γ assays were performed using the whole blood Bovigam™ ELA bovineinterferon test, which is suitable for the detection of ovine IFN-γ. Thetest was performed as per the manufacturer's (Commonwealth SerumLaboratories, Australia) instructions, with some modifications. Briefly,blood samples were collected in lithium heparin tubes and processedwithin 4 hours of collection.

For each antigen to be tested, 1 ml aliquots of blood were dispensedinto 24-well tissue culture hays. Routinely, antigens were tested induplicate. Each antigen was added in a standard volume of 67 μl to theblood aliquots and mixed for 5 min on a rotating platform shaker. Thetrays were then incubated 22 h at 37° C. in a humidified atmosphere with5% CO₂. From each blood/antigen aliquot, 200 μl of plasma was harvestedand stored at −20° C. in 96-well plates for subsequent testing. Theplasma samples were assayed singly for IFN-γ using Bovigam™ EIA platesaccording to the manufacturer's instructions. Absorbance readings werecarried out on a MAXline, Vmax® (Molecular Devices Corp., USA) kineticmicroplate reader at 450 nm.

Johnin PPD or Avian PPD (Commonwealth Serum Laboratories, Australia) wasused at 12.5 μg/n as a positive control for specific stimulation. PBSwas included as a negative control. For all assays, the non-specificT-cell stimulator concavalin A (Sigma, USA) was included for all animalsat 20 μg/ml to check cell viability.

Results were expressed as “corrected” absorbance at 450 nm. Forduplicate wells, this was defined as the average A_(450 nm) of thestimulated wells (Avian or Johnin PPD or protein of the invention) minusthe average A_(450 nm) of the PBS control wells. For single the proteinof the invention stimulated wells, this was defined as the A_(450 nm) ofthe stimulated well minus the average A_(450 nm) of the PBS controlwells. Differences between groups were calculated by the Mann-Whitneytest. The software package InStat 2.01 (GraphPad Software Incorporated,USA) was used for statistical analysis.

Results

Cell-Mediated Immune Responses to the Protein of the Invention

To investigate if recombinant protein could stimulate cell-mediatedimmune (CMI) responses in Neoparasec-vaccinated animals, whole bloodIFN-γ assays were carried out. In the first instance, Ni⁺²-affinityenriched recombinant protein was tested in single wells in threedifferent concentrations (2.6 μg, 0.64 μg and 0.32 μg). Results areshown in FIG. 7. There was a significant difference (pc<0.01) betweenthe Neoparasec-vaccinated and unvaccinated group in the IFN-γ responsesto protein of the invention at all three concentrations. Eight of thenine vaccinated animals showed IFN-γ production to all threeconcentrations of protein, often in a concentration-dependent manner.Animal 136 had very low IFN-γ production to protein and to Avian PPD.The low response to Avian PPD was consistent in this animal over theprevious five months of testing (data not shown). None of theunvaccinated animals had notable IFN-γ responses to the protein of theinvention, however, three of these animals (128, 133, 569) hadcomparatively large responses to Avian PPD, especially animal 569.Reactions of control animals to Avian PPD were not uncommon and appearedoccasionally in various animals during testing over the previous fivemonths (data not shown).

To demonstrate that the immunologically active component in theNi⁺²-affinity preparation was the protein of the invention, the proteinwas purified by size-exclusion chromatography and tested for its abilityto stimulate IFN-γ production in whole blood. Results are shown in FIG.8. There was a significant difference p<0.05) in the IFN-γ responses to1 μg of the protein of the invention between the vaccinated andunvaccinated group, despite the low responses of animals 578 and 587 inthe vaccinated group and the notable response in animal 133 in theunvaccinated group. Animal 136 was not included in the assay because ofits consistently poor response to Avian and Johnin PPD. To see if theIFNI production to the protein of the invention wasconcentration-dependent, three vaccinated animals were chosen from Mob1, along with three unvaccinated animals for testing using 5 μg ofpurified protein. Only three animals from each group were tested due tolimited amounts of purified protein. Two animals in the vaccinated grouphad evident concentration-dependent responses to the antigen and thethird had a slight concentration-dependent response.

EXAMPLE 5

Localisation of the Protein of the Invention in M. ptb

An indirect approach to investigate whether the protein of the inventionis exported in its native host, M. ptb, was to determine if animalsvaccinated with M. ptb strain 316F culture filtrate produced antibody tothe protein.

Materials and Methods

The techniques used herein were as described in Example 4 above.

Results

Detection of the Protein With Serum From Sheep Vaccinated with M. ptbStrain 316F Culture Filtrate

Serum samples from M. ptb culture filtrate-vaccinated sheep were used toprobe individual Western blots of recombinant protein. Results are shownin FIG. 9.

All five vaccinated animals had antibodies to the antigen at one monthpost-vaccination. Antibody was not present prior to vaccination

EXAMPLE 6

Localisationi of the Protein in M. ptb

A direct approach to investigate whether the protein of the invention isexported in its native host, M. ptb, was to determine its location inWestern blots of culture filtrate fractions using rabbit antibody raisedto the protein.

Materials and Methods

Preparation of the Protein for Immunisation

The protein of the invention was prepared for inununisation bytransferring approximately 0.05 mg of Ni⁺²-affinity enriched recombinantprotein onto nitrocellulose membrane. The membrane was stained withPonceau S and the protein band was excised, destained and air-dried. Theblot was then fragmented inside a microfuge tube with the aid of asterile scalpel blade. To this, approximately 300 μl of PBS was addedand the material was further fragmented until it could pass through an18 gauge, 1½” needle. Five hundred microlitres of Freund's incompleteadjuvant (F 5506, Sigma, USA) was added and the mixture was passedthrough the needle several times before being injected.

Rabbit Immunisation Protocol

Adult New Zealand White rabbits were individually housed under standardconditions in outdoor hutches by Agricultural Services, MasseyUniversity, Palmerston North, New Zealand. Injection of prepared antigenwas done subcutaneously in the mid-scapular skin fold of one rabbit.This was repeated *approximately three weeks later. To check forantibody production, 5 ml of venous blood was collected from theexternal ear by a scalpel nick three weeks after the second injection.Serum was harvested from the clotted blood after centrifugation at3,000×g for 15 min. At the same time, serum was similarly collected froma naïve rabbit for use as control serum. The sera were aliquotted andstored at −20° C. Following confirmation of antibody production, therabbit was exsanguinated and serum was harvested as above

Results

Production of Rabbit Antibody Raised to the Protein and Detection of theProtein in Cellular Fractions

To determine the cellular localisation of the native protein of theinvention in M. ptb strain 316F, rabbit antibody was raised torecombinant protein. As shown in FIG. 10, the anti-serum recognisedrecombinant protein on Western blots. Naïve rabbit serum did notrecognise the protein. The serum was used to probe Western blots ofequivalent amounts of M. ptb strain 316F culture filtrate. Results areshown in FIG. 11. A single band of apparent molecular weight 24.2 kDawas detected in the culture filtrate, which was slightly larger than themolecular weight of 22.3 kDa calculated for the maure native proteinbased on its amino acid composition. This band was also present ingreater intensity in both the soluble and insoluble cell preparations.Several other weak bands of higher molecular weight were produced in thesoluble and insoluble cell fractions with the naïve and recombinantprotein-immunised rabbit sera Comparison to Ni⁺-affinity chromatographyprepared recombinant protein produced from M. smegmatis, previouslyshown to migrate with an apparent molecular weight of 23 kDa, confirmednative protein migrated slightly slower than recombinant protein.

EXAMPLE 7

To determine if sequences related to the gene encoding the protein ofthe invention existed in other mycobacterial species, nucleic aciddatabase searches, PCR and Southern blot analyses were carried out

Materials and Methods

PCR Amplification of the Protein-Encoding ORF From Genomic DNA

PCR amplifications were carried out on mycobacterial genomic DNA usingthe primer pairs 1pp27-fBam and 1pp27-rKpn. The reactions were carriedout in 20 μl using Taq DNA polymerase. Template DNA consisted of 2 μl ofa 1:50 dilution of purified DNA or, alternatively, single bacterialcolonies were added directly to the PCR mixture.

Southern Blotting and Hybridisations

Approximately 1 μg of restriction endonucleasedigested genomic DNAfragments were electrophoresed in 0.7% agarose gels and transferred tonylon membranes (Biodyne B, Gelman, Pall Corporation, USA) by capillarytransfer using standard procedures (Sambrook et al., 1989). The DNA wasfixed to the membrane by exposure to UV light for 4 min using a Bio-RadGel Doc 2000 transilluminator (Bio-Rad, USA). Fixed membranes wereprehybridised in heat-sealed plastic bags with:DIG Easy Hyb buffer(Roche Molecular Biochernicals, Germany) at 42° C. for 2 h with constantshaking in a Hot Shaker water bath (Bellco Biotechnology, N.J., USA).Hybridisation was done in the same buffer at 2.5 ml/100 cm² with 25-50ng/ml of denatured DIG-labeled probe DNA at 40° C. for 18 h. Thehybridised membranes were washed 2×5 min in 2×SSC, containing 0.1% (w/v)SDS at room temperature, followed by 2×5 min washes in 0.7×SSCcontaining 0.1% (w/v) SDS at 68° C. with constant shaking.Immunodetection of hybridised probe was achieved using the DIG system(Roche Molecular Biochemicals, Germany). Briefly, washed membranes wereincubated in 1 ml/cm² blocking solution (Roche Molecular Biochemicals,Germany) for 60 min at room temperature with shaking. The blockingsolution volume was reduced to 20 ml/100 cm² and anti-DIG antibodyconjugated to alkaline phosphatase (Roche Molecular Biochemicals,Germany) was added to a final dilution of 1:10,000 according to themanufacturer's recommendations. The blots were developed bychemiluminescence with CSPD or CPD-Star substrate (NEN, MA, USA). Thedeveloped blots were exposed to radiographic film (BioMax MR, Kodak,USA) for 5 min to 18 h, depending on signal intensity, in the presenceof a single intensifying screen (Kodak Lanex Regular, Kodak, USA). Filmwas developed in an automated processor (Kodak RP X-OMAT Processor ModelM6B).

DNA Probe Preparation

All probes were labeled by the incorporation of DIG-labeled dUTP(DIG-11-dUTP, Roche Molecular Biochernicals, Germany) during PCR.DIG-11-dUTP (1 573 152, Roche Molecular Biochemicak, Germany) was addedto a final concentration of 20 μM in a reaction volume of 50 μl and dTTPwas adjusted to a final concentration of 80 μM. All otherdeoxynucleoside triphosphates were added to 100 μM. To estimate thepurity and yield of DIG-labeled product, approximately 2 μl of thereaction was electrophoresed in agarose gels alongside a mass ladder forquantitation (10068-013 Low Mass DNA Ladder, Life Technologies Inc.,USA). Due to the presence of DIG, the PCR products routinely appearedlarger than unlabeled products. For quantitation of DIG-incorporation inprobes, side-by-side filter spot tests, ranging from 0.01 pg to 10 pg,were carried out as per the manufacturer's recommendations. Labeled PCRproducts were stored at −20° C. until used for hybridisation.

Results

PCR Amplifcation of the Gene Encoding the Protein From Mycobacteriumspecies and Strains

To determine if the gene encoding the protein of the invention waspresent in other M. ptb strains, several isolates representing fiveIS900 RFLP types (Collins et al., 1990) were used in PCR analyses. Theresults are shown in FIG. 12. The expected 725 base pair product wasamplified from all 13 isolates.

To investigate the species distribution of the gene encoding the proteinof the invention within the genus Mycobacterium, PCR reactions werecarried out with a limited number of mycobacterial species, includingtwo strains of M. ptb and 11 strains from the M. tuberculosis complex.Primers 1pp27-fBam and 1pp27-rKpn were used. Amplification of thegenus-specific 16S rRNA gene was carried out in parallel for all DNAspecies and served as a positive control for the reactions. Annealingtemperatures of 55° C. and 62° C. were employed (the calculated Tm ofthe primers was 66° C. in 50 mM NaCl). Results are shown in FIG. 13. PCRproducts of the expected size (725 base pairs) were amplified from bothof the M. ptb isolates as well as M. scrofulaceum and M intracellulareusing both annealing temperatures. The only other product of theexpected size for the gene of interest was produced at 55° C., in the M.tubercuosis complex strains (FIG. 13 b; lanes 12-22), however thisproduct was very weak and was not produced at 62° C. A major band it 250base pairs was produced with M. terrae at 55° C., however this productwas not produced at 62° C. Various weak products were amplified fromseveral of the other species, but none of these were produced withconsistency at both annealing temperatures.

Southern Blot Detection of Gene of Interest in Mycobacterium Species andStrains

Southern blot analyses were performed with Bam HI-digested genomic DNAsfrom 13 Mycobacterium spp. The ORF encoding the protein of the inventionwas used as probe and was labeled by incorporation of DIG-dUTP duringPCR using the primers 1 pp27-fBam and 1pp27-rKpn. FIG. 14 shows theprobe hybridised strongly to a single band, approximately 2,200 basepairs in length from M. ptb 316F and a slightly larger band of 2,300base pairs from M. ptb ATCC 53950. The probe also hybridised weakly to a1,000 base pair band from M. intracellularae. Upon overnight exposure(data not shown), a weak band at approximately 10,000 base pairs waspresent in M. marinum, M terrae, M pheli and M. kansasii. Hybridisationwas not detected with M. bovis, M. tuberculosis, or M. bovis BCG.

EXAMPLE 8

To enable ease of production of the protein of the invention in greaterquantities, an expression system utilizing E. coli was developed. Theprotein of the invention so produced was used in a vaccination trial toanalyse it's ability to engender an immune response.

Materials and Methods

Animals and Handling

The ovine model consisted of 17, 8 month old, Romney wether (castratedmale) lambs. All vaccinations were administered subcutaneously to theright hand side of the neck using 0.6 mm×12 mm needles. Animalsvaccinated with protein of the invention were kept under observation for1 hr following vaccination, and then checked 3 hrs post vaccination toverify that there were no adverse reactions to the recombinant vaccine.

Construction of pPet22

pPET22 is pET14b (Novagen) containing the gene sequence encoding theprotein of the invention devoid of the first 57 bases that encode thesecretion signal. The 648 bp sequence was obtained from pMIP12 by PCRamplification using the primers P22-SF(5′-GGGAATTCCATATGTTGATCGCCGGCTGCTCGTCGGG C-3′, SEQ ID NO. 8), andP22-SR (5′-GGGAATTCCATATGTCACGAGCTCA CCGGGGGCTTGGTG-3′, SEQ ID NO.9),with Pfu Turbo DNA polymerase (Strategene).

The amplified product containing NdeI restriction sites was purifiedfrom an agarose gel using the QIAquick PCR purification protocol.Following digestion with NdeI, the fragment was ligated into NdeIdigested pET14b and the resulting plasmid was used to transform E. coliBL21-CodonPlus cells (Strategene) using standard procedures.

Affinity Purification and Concentration of Recombinant Protein

Recombinant protein of the invention was isolated from the induced E.coli strain BL21-CodonPlus containing the plasmid pPET22 (i.e. theexpression strain) using the materials and methods provided by theProBond purification system version F (Invitrogen, Carlsbad Calif.,USA).

In brief, cells were lysed under protein denaturing conditions byresuspending cell pellets in a buffer containing 6 M guanidinehydrochloride, 20 mM sodium phosphate, and 500 mM sodium chloride andwith a pH of 7.8. RNA and DNA were sheared by sonication to reduceviscosity, and this was followed by centrifugation at 3,000×g for 15minutes to remove insoluble debris. The lysate supernatant was mixedwith the ProBond resin. The mixture was then centrifuged to separate theresin from the lysate. The lysate was removed, and the resin was washedseveral times with the following wash buffers:

-   -   1. Denaturing binding buffer; 8 M urea, 20 mM sodium phosphate        500 mM sodium chloride, pH 7.8,    -   2. Denaturing wash buffer 6.0; 8 M urea, 20 mM sodium phosphate        500 mM sodium chloride, pH 6.0,    -   3. Denaturing wash buffer 5.3; 8 M urea, 20 mM sodium phosphate        500 mM sodium chloride, pH 5.3.

Following each washing step, the wash mix was centrifuiged to separatethe resin from the wash buffer. The samples were then eluted byresuspending the resin several times in Denaturing elution buffer; 8 Murea, 20 mM sodium phosphate 500 mM sodium chloride, pH 4.0.

The wash and elution fractions were analysed by SDS-PAGE to determinewhich fractions contained purified protein of the invention. Fractionscontaining purified protein of the invention were then pooled togetherand dialyzed against PBS and urea by incrementally reducing theconcentration of urea in the dialysis buffer by 1 M each time the bufferwas changed until urea concentration was below 0. 1 mM.

Protein of the invention was concentrated by ultrafiltration, andsterility was verified by inoculating blood agar plates with the proteinsolution (˜100 μl of concentrated protein solution streaked across athird of a blood agar plate) and incubating for up to 1 week at 37° C.Samples showing no bacterial growth were considered suitable for ovinetesting.

Concentrated protein samples were also submitted to the Institute ofEnvironmental Science & Research Limited, New Zealand for determinationof endotoxin quantities using the LAL (Limulus Amoebocyte Lysate) test(Associates of Cape Cod Inc. USA).

Vacciiation Trials

A total of 17 sheep were used for the protein of the inventionvaccination trial testing (Table 2). Six animals were vaccinated with 1ml of the commercially available Neoparasec vaccine (Merial Ltd.). Fiveanimals were vaccinated with 0.8 mg of the recombinant protein of theinvention mixed approximately 1:1 (v/v) with Neoparasec adjuvant for atotal volume of 2 ml. Six animals were used as an unvaccinated controlgroup. TABLE 2 Vaccination Sheep Weight Group weight Vaccine Date No.(kg) average (kg) Control group N/a 37.1 none 808 39.1 none 823 39.3none 830 39.4 none 834 37.9 none 863 31.9 none 869 34.7 Neoparasec groupJan. 30, 2003 38.2 Neoparasec 811 36.2 Neoparasec 813 43.9 Neoparasec817 38.7 Neoparasec 819 37.5 Neoparasec 821 37.1 Neoparasec 854 35.8Recombinant Apr. 16, 2003 38.1 protein group protein 820 37.2 protein825 39.7 protein 828 36.1 protein 829 36.1 protein 848 41.3

Western Blotting

Purified protein of the invention (133 μg protein/ml) was added at 3 μlper well on 15% SDS-PAGE gels. Following electrophoresis, the protein onthe gel was blotted to a PVDF membrane using a Trans-Blot SD Semi-DryTransfer Cell (BioRad, USA). The membranes were stained with Ponceau Sto verify that protein transfer had taken place. The membranes were thendestained with deionized H₂O, and blocked overnight in 5% (w/v) skimmilk at 4° C.

Following blocking thin strips corresponding to lanes of the originalgel were cut and placed separately in plastic trays. Serum samples fromsheep vaccinated with the protein of the invention, Neoparasec andnon-vaccinated control sheep were added separately to a membrane stripafter diluting 1:500. These strips were incubated for 1 hr at roomtemperature followed by washing several times to remove any unboundserum. The strips were then incubated in peroxidase conjugatedanti-sheep IgG secondary antibody diluted 1:40,000. The strips werewashed several times to remove any unbound antibody, and SuperSignalWest Femto Maximum Sensitivity Substrate (Pierce Scientific, USA) wasadded to the membrane, followed by exposure to BioMax scientific imagingfilm (Kodak, 20 USA) for time periods of 5, 15, 30, 60, and 180 secondsfollowing which the film was immediately developed.

Measuring IFN-γ Production From Sheep Vaccinated With Protein of theInvention

Five weeks following vaccination with the protein of the invention, eachsheep had approximately 8 ml of blood -collected into a 10 ml Vacutainertube containing lithium heparin (Beckton Dickinson, UK). Also at thistime, two sheep that had received Neoparasec vaccine and two that wereunvaccinated were also bled.

Duplicate 1 ml aliquots of each sample were incubated for 20 h withthese antigens at the given concentrations: PBS (negative control), PPDA 12.56 μg/ml, protein of the invention 10 μg/ml, and a single aliquotof Concavalin A-Con A (positive control) 20 μg/ml. Following incubation,approximately 200 μl of the cytokine containing plasma was removed andplaced in a 96 well tray: 50 μl of this plasma was then used to performa Bovigam Tm Bovine Gamma Interferon Test, (CSL, Australia, batch no:0300-07001).

ELISA for the Quantification of Serum Antibodies Specific to the Proteinof the Invention

A protein of the invention-adsorbed enzyme-linked inmnunosorbent assay(ELISA) was used to measure the level of antibodies (5 weeks postvaccination) that had been raised specifically against the protein ofthe invention.

The recombinant protein of the invention was purified under denaturingconditions using a nickel affinity column (ProBond, Invitrogen, Calif.,USA) according to manufacturer's instructions. Following fiberpurification through a Sephadex 75 HR 10/30 column, protein of theinvention was adsorbed onto 96 well microtitre plates (DynexTechnologies Inc, Virginia, USA) at a concentration of 0.15 μg/well.Plates were blocked overnight at 4° C. with 5% (w/v) millk powder in PBS(blocking buffer) added to each well (200 μl/well) before washing 3times with PBS containing 0.05% (v/v) Tween-20; followed by one washwith PBS.

Serum collected from Neoparasec (animals 811, 813, 817, 819, and 821),protein of the invention (animals 820, 825, 828, 829 and 848) ornon-vaccinated animals (animals 808, 823, 830, 834, 863 and 869) werepre-diluted 1:200 or 1:800 in blocking buffer before being added to eachwell (100 μl/weU) in duplicate. As a negative control (background),blocking buffer was added to wells instead of test sera Followingincubation for 1 h at 37 ° C., unbound antibodies were removed bywashing as previously described. Bound antibodies were detected with 100μl/well of alkaline-phosphatase conjugated donkey anti-sheepimmunoglobulin (Sigma, Virginia, USA), diluted 1:30000 in PBS andincubated for 1 h at 37 ° C. The plates were washed as described, andthe reaction developed with p Nitrophenyl Phosphate (PNNP, Sigma, USA),1 mg/ml in 10% diethanolamine buffer, pH 9.8, containing 0.5 MM MgCl₂.

After a 25 min incubation, measurements were obtained by reading theabsorbance at OD₄₀₅ using an ELISA plate reader (Vmax, Molecular DevicesCorp., California, USA). The reaction was then stopped by adding 100μl/well of 2 M sodium carbonate solution. Mean optical densities werecalculated for each duplicate sample and these were corrected bysubtraction of the mean OD₄₀₅ of their respective negative controlwells.

Results

Preparation of Recombinant Protein of the Invention

Affinity purified protein of the invention was made in 6 separatebatches recorded as MB1 a, MB1 b, MB1c, DB1, DB2, and DB3. These werecombined to yield a final volume of 4.8 ml having a proteinconcentration of 0.799 mg/ml. The purity of this sample was determinedbased on SDS-PAGE analysis of the protein samples following purification(FIG. 15).

The endotoxin test reported that the sample (MB1b) had 10⁵ EU (endotoxinunits)/ml (results from Environmental Science & Research Limited, NewZealand 3/26/2003). Since 1 EU=0.1 ng endotoxin (Environmental Science &Research Limited, New Zealand), then 10⁵ EU=10⁴ ng of endotoxin or 10μg, and the concentration of endotoxin in the sample was 10μg/ml orabout 31 μg endotoxin/mg protein as determined using the protein assaymethod of Bradford.

Cell Mediated Immune Response to the Protein of the Invention

Five weeks after the vaccination blood was drawn from five animals ofeach group to compare protein of the invention-specific cell mediatedimmune responses and humoral immune responses. Using IFN-γ production asan indicator of a cell mediated response, the results (FIG. 16)demonstrate that the group vaccinated with the protein of the inventionelicits a cellular immune response when stimulated in vitro with proteinof the invention in four out of the 5 animals (solid black bars) ascompared with the non-vaccinated sheep.

Humoral Immune Response

Western blot and ELISA were used to test for the presence of antibodiesspecific to the protein of the invention in the group vaccinated withthe protein of the invention, as compared to the Neoparasec vaccinatedand non-vaccinated groups.

Western blot analysis using serum from five animals in each of the threegroups (FIG. 17) shows that 4 out of the 5 animals belonging to thegroup vaccinated with the protein of the invention elicited a stronghumoral response against recombinant protein of the invention (animalnumbers 825, 820, 828, and 829), and one had a very weak- response(number 848). 4 of the 5 Neoparasec vaccinated sheep demonstrated astrong humoral response (animal numbers 811, 813, 817, and 819), whileone showed a weak response (number 821). None of the control animalsgave a significant response to the protein of the invention antigen.Analysis by ELISA (see FIG. 18 and 19) clearly demonstrates that at 5weeks post vaccination, the animals vaccinated with Neoparasec and thosevaccinated with the protein of the invention elicited a significantprotein of the invention-specific antibody response. Antibody responsesin some animals vaccinated with the protein of the invention matchedthat of the Neoparasec (positive control) vaccinees. As expected,further dilution of the antibody from 1in 200 to 1 in 800 decreased theOD values for all the animals.

It will be appreciated that the above description is provided by way ofexample only and that the variations in both the materials and thetechniques used which are known to those persons skilled in the art arecontemplated.

1. A recombinant, purified, or isolated polypeptide comprising an aminoacid sequence selected from (a) the sequence of SEQ ID No: 1; (b) afunctionally equivalent variant of the sequence of SEQ ID NO: 1 whichhas greater than 77% amino acid sequence identity with SEQ ID NO: 1; and(c) a functionally equivalent fragment of a polypeptide defined in (a)or (b).
 2. A recombinant, purified, or isolated polypeptide comprisingan amino acid sequence selected from (a) amino acids 20 to 235 of SEQ IDNO: 1 (b) a functionally equivalent variant which has greater than 77%amino acid sequence identity with amino acids 20 to 235 of SEQ ID NO: 1;and (c) a functionally equivalent fragment of a polypeptide defined in(a) or (b).
 3. A polypeptide as claimed in claim 2 wherein the sequencehas greater than 90% identity with SEQ ID NO:
 1. 4. A polypeptide asclaimed in claim 2 wherein the sequence has greater than 99% identitywith the sequence of amino acids 20 to 235 of SEQ ID NO:
 1. 5. Apolypeptide as claimed in claim 2 wherein the sequence is that of aminoacids 20 to 235 of SEQ ID NO:
 1. 6. A polypeptide as claimed in claim 1which is obtainable from a bacterium.
 7. A polypeptide as claimed inclaim 1 which is obtainable from Mycobacterium avium subspeciesparatuberculosis.
 8. A polypeptide as claimed in claim 1 which isobtainable from a heterologous host transformed with a polynucleotidewhich encodes said polypeptide or functionally equivalent variant orfragment thereof wherein said host is capable of expressing saidpolypeptide.
 9. A polypeptide as claimed in claim 8 wherein the host isE. coli.
 10. A genetic construct comprising (a) a promoter sequence; (b)an open reading frame polynucleotide encoding a polypeptide as claimedin claim 1 ; (c) a termination sequence.
 11. A recombinant, purified, orisolated polynucleotide comprising the sequence of SEQ ID NO: 2 or avariant thereof encoding either the polypeptide comprising the aminoacid sequence of SEQ ID NO: 1 or a functionally equivalent fragment ofsaid polynucleotide.
 12. A recombinant, purified or isolatedpolynucleotide with a nucleotide sequence complementary to thepolynucleotide of claim
 11. 13. One or more oligonucleotide orpolynucleotide primers capable of amplifying a polynucleotide whichencodes a polypeptide as claimed in claim 1 in a Polymerase ChainReaction or other polynucleotide amplification method.
 14. A purified orisolated antibody capable of binding a polypeptide as defined in claim4.
 15. A vaccine composition comprising a polypeptide as claimed inclaim 1 and an acceptable diluent, carrier, excipient, or adjuvant, saidpolypeptide being present in an amount sufficient to generate aprotective immune response to Mycobacterium avium subspeciesparatuberculosis infection.
 16. A diagnostic composition for use indetecting the presence of Mycobacterium avium subspeciesparatuberculosis, wherein said composition comprises a polypeptide asclaimed in claim
 1. 17. A diagnostic composition for detecting thepresence of Mycobacterium avium subspecies paratuberculosis, whereinsaid composition comprises a polynucleotide according to claim
 11. 18. Adiagnostic composition for detecting the presence of Mycobacterium aviumsubspecies paratuberculosis comprising at least one oligonucleotide orpolynucleotide primer capable of amplifying a polynucleotide whichencodes a polypeptide as claimed in claim in a Polymerase Chain Reactionor other polynucleotide amplification method.
 19. A diagnosticcomposition for detecting the presence of Mycobacterium avium subspeciesparatuberculosis comprising an antibody according to claim
 14. 20. Amethod of detecting Johne's disease including preclinical Johne'sdisease in an animal comprising contacting either the animal or a samplefrom the animal with a polypeptide as claimed in claim 1 and detectingan immune response indicative of the presence of Mycobacterium aviumsubspecies paratuberculosis.
 21. A method according to claim 20 whereinthe response is a delayed-type hypersensitivity response.
 22. A methodaccording to claim 20 wherein said detecting comprises detecting thepresence of antibodies that bind a recombinant, purified, or isolatedpolypeptide comprising an amino acid sequence selected from (a) aminoacids 20 to 235 of SEQ ID NO: 1; (b) a functionally equivalent variantwhich has greater than 99% amino acid sequence identity with amino acids20 to 235 of SEQ ID NO: 1; and (c) a functionally equivalent fragment ofa polypeptide defined in (a) or (b) .
 23. A method according to claim 22wherein the detection of the presence of antibodies is by ELISA,radioimmunoassay or Western blotting.
 24. A method of detecting Johne'sdisease including preclinical Johne's disease in an animal comprisingcontacting a sample from the animal either with a purified or isolatedantibody capable of binding a recombinant, purified, or isolatedpolypeptide comprising an amino acid sequence selected from (a) aminoacids 20 to 235 of SEQ ID NO: 1, (b) a functionally equivalent variantwhich has greater than 99% amino acid sequence identity with amino acids20 to 235 of SEQ ID NO: 1, and (c) a functionally equivalent fragment ofa polypeptide defined in (a) or (b); or a composition comprising anantibody specific to the recombinant, purified, or isolated polypeptidecomprising an amino acid sequence selected from (a) amino acids 20 to235 of SEQ ID NO: 1, (b) a functionally equivalent variant which hasgreater than 99% amino acid sequence identity with amino acids 20 to 235of SEQ ID NO: 1, and (c) a functionally equivalent fragment of apolypeptide defined in (a) or (b); and detecting a polypeptide whichbinds to the antibody.
 25. A method according to claim 24 wherein thepresence of bound antibody is determined by ELISA, radioimmunoassay orWestern blotting.
 26. A method according to claim 24 for detecting thepresence of Mycobacterium avium subspecies paratuberculosis at apreclinical phase of Johne's disease.
 27. A method of detecting Johne'sdisease including preclinical Johne's disease in an animal comprisingcontacting a sample from the animal with a composition comprising of atleast one oligonucleotide or polynucleotide primers capable ofamplifying a polynucleotide which encodes a polypeptide as claimed inclaim 4 in a polynucleotide amplification method and detecting theamplification product.
 28. A method as claimed in claim 27 wherein thepolynucleotide amplification method is a polymerase chain reactionmethod.
 29. A method according to claim 22 for detecting the presence ofMycobacterium avium subspecies paratuberculosis at a preclinical phaseof Johne's disease.
 30. A method of detecting Johne's disease in ananimal comprising contacting a sample from the animal with a compositioncomprising a polynucleotide capable of binding to a polynucleotide whichencodes a polypeptide as claimed in claim
 4. 31. A method according toclaim 30 wherein said polynucleotide is detectably labeled.
 32. A methodaccording to claim 31 wherein said detectable label is a radioisotope orfluorescent tag.
 33. A method of prophylactically or therapeuticallytreating an animal against Johne's disease which comprises administeringto an animal a polypeptide as claimed in claim 1 to produce a protectiveimmunological response in the animal.
 34. A method according to claim 33which is a therapeutic method.
 35. A method according to claim 33 whichis a prophylactic method.
 36. A method of vaccinating against Johne'sdisease which comprises administering to an animal a vaccine compositionas claimed in claim 15 in an amount sufficient to produce a protectiveresponse.
 37. A method according to claim 36 wherein said administrationis performed on a single occasion.
 38. A method according to claim 36wherein said administration is performed on more than one occasion. 39.A method as claimed in claim 3 wherein
 0. 1-100011 G/KG is administeredof a recombinant, purified, or isolated polypeptide comprising an aminoacid sequence selected from (a) the sequence of SEQ ID No: 1; (b) afunctionally equivalent variant of the sequence of SEQ ID NO: 1 whichhas greater than 77% amino acid sequence identity with SEQ ID NO: 1; and(c) a functionally equivalent fragment of a polypeptide defined in (a)or (b).
 40. A method as claimed in claim 39 wherein 5-500μG/KG of thepolypeptide is administered.
 41. A kit for use in detecting the presenceof Mycobacterium avium subspecies paratuberculosis comprising at leasttwo of the following: a polypeptide as claimed claim 1; an antibody thatbinds said polypeptide, and a reagent for determining antigen-antibodybinding.
 42. A host cell transformed with a polynucleotide of claim 11 .43. A vector comprising the construct as claimed in claim
 10. 44. A hostcell incorporating a construct of claim
 10. 45. A host cellincorporating a vector as claimed in claim
 43. 46. A host cell accordingto claim 45 wherein said vector exists within the host cell as aplasmid.
 47. A host cell according to claim 45 wherein said vector isintegrated into the genome of the host cell.
 48. A method as claimed inclaim 20 wherein the animal is a ruminant.
 49. A method as claimed inclaim 47 wherein the animal is a sheep.
 50. A method as claimed in claim33 wherein the animal is a ruminant.
 51. A method as claimed in claim 50wherein the ruminant is a sheep.